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<h3>

Michael R. Crusoe pushed to branch master

at <a href="https://salsa.debian.org/med-team/cwltool">Debian Med / cwltool</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/cwltool/commit/91ec6ace8b42af7fb581b8ef2304d58556aa61ef">91ec6ace</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-09-15T19:17:18Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.20190915164430+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/cwltool/commit/c6041ba785562e95f71c52f2490a478dc28be86d">c6041ba7</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-09-15T19:17:19Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.0.20190915164430+dfsg'

Update to upstream version '1.0.20190915164430+dfsg'

with Debian dir 1749ba7f4c0fc45d14605e867f01402c3a8bf2f9</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/cwltool/commit/b5a53e1c357c3f9071e67eb6ab6507e22ac2d141">b5a53e1c</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-09-15T19:34:33Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version

</pre>

</li>

</ul>

<h4>30 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

Makefile

</a>

</li>

<li class="file-stats">

<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">

PKG-INFO

</a>

</li>

<li class="file-stats">

<a href="#561b88e19de321ca62c7590bbb350765fb110905">

README.rst

</a>

</li>

<li class="file-stats">

<a href="#b56b7a64ee5cdb86aa33e58c869fc85468a88dfe">

cwltool.egg-info/PKG-INFO

</a>

</li>

<li class="file-stats">

<a href="#0f5f9a487de6f81f4140b1291f27031478a7b0b2">

cwltool.egg-info/SOURCES.txt

</a>

</li>

<li class="file-stats">

<a href="#f37416a929e52b34959bfb17948722683d25dca6">

cwltool/argparser.py

</a>

</li>

<li class="file-stats">

<a href="#157096f5f986f141b1bd83003c5b5ce452ecd020">

cwltool/builder.py

</a>

</li>

<li class="file-stats">

<a href="#255ee49f33c79c25f6a55971fe53bd72a9fb8575">

cwltool/executors.py

</a>

</li>

<li class="file-stats">

<a href="#1a4debaa3574d5d928e4fc1d259929cac851b4b6">

cwltool/job.py

</a>

</li>

<li class="file-stats">

<a href="#ef56fd169f82fcdcb5c4e7b80a7164f20004c766">

cwltool/main.py

</a>

</li>

<li class="file-stats">

<a href="#16fce72f6e9f404418a9d668d41e4181bb3abe61">

cwltool/provenance.py

</a>

</li>

<li class="file-stats">

<a href="#e4186687ed9ace3055434ea5fdd184601e544d69">

cwltool/singularity.py

</a>

</li>

<li class="file-stats">

<a href="#981a72379b95d1fc9d93c9d8380918dd3ab82e9e">

cwltool/workflow.py

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#fcb92b9accd9db58b837ef9c16090c7d4830a9f9">

debian/patches/disable_prov

</a>

</li>

<li class="file-stats">

<a href="#986d91bafce8bbac47e11e9d329955f76890bf0b">

debian/patches/pytest

</a>

</li>

<li class="file-stats">

<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">

debian/tests/control

</a>

</li>

<li class="file-stats">

<a href="#aab2726ed6daf419caf178b1480b6d7da8a85af6">

debian/tests/run-tests

</a>

</li>

<li class="file-stats">

<a href="#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">

setup.cfg

</a>

</li>

<li class="file-stats">

<a href="#48a232f5e05cbaa234aa30dfa88a8d19bc10a1bc">

<span class="new-file">

+

tests/arg-empty-prefix-separate-false.cwl

</span>

</a>

</li>

<li class="file-stats">

<a href="#6114135dd99d21b62b938d64cf9260a92d1f1416">

tests/env.cwl

</a>

</li>

<li class="file-stats">

<a href="#98c1e4d87524a5347c05bae01246f5c25bd6bd48">

<span class="new-file">

+

tests/env2.cwl

</span>

</a>

</li>

<li class="file-stats">

<a href="#a4d3b8d2921c82c34c5afa41066477aba090b135">

tests/secondary-files-string-v1.cwl

</a>

</li>

<li class="file-stats">

<a href="#c850a901a4677d28f381ddf53272d079cf0d4ae0">

tests/test_examples.py

</a>

</li>

<li class="file-stats">

<a href="#7593f63b8b7959e775e8a25fcf434451b4da06a7">

tests/test_provenance.py

</a>

</li>

<li class="file-stats">

<a href="#6a7cf45dc67d70001b23638ee84abceec3fe8f84">

tests/test_toolargparse.py

</a>

</li>

<li class="file-stats">

<a href="#172f21b418c7d70b9e17cff1ed0fc4d6036b4d7f">

tests/test_udocker.py

</a>

</li>

<li class="file-stats">

<a href="#4f5e5d8e9fca25e91732fa82113435fd58ffbc58">

tests/trs/md5sum-workflow.cwl

</a>

</li>

<li class="file-stats">

<a href="#e3a2c135872245be444d76de339dc087b299d383">

tests/wf/optional-numerical-output-0.cwl

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,12 +34,6 @@ VERSION=1.0.$(shell TZ=UTC git log --first-parent --max-count=1 \</td>

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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make">  <span class="nt" style="color: #000080;">--format</span><span class="o" style="font-weight: 600;">=</span>format:%cd <span class="nt" style="color: #000080;">--date</span><span class="o" style="font-weight: 600;">=</span>format-local:%Y%m%d%H%M%S<span class="nv" style="color: #008080;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

35

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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

35

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="nv" style="color: #008080;">mkfile_dir</span> <span class="o" style="font-weight: 600;">:=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">dir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>abspath <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>lastword <span class="nv" style="color: #008080;">$(MAKEFILE_LIST)</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"><span class="nv" style="color: #008080;">UNAME_S</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">uname</span> <span class="nt" style="color: #000080;">-s</span><span class="nv" style="color: #008080;">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(UNAME_S),Linux)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC38" class="line" lang="make">  <span class="nv" style="color: #008080;">nproc</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">nproc</span><span class="nv" style="color: #008080;">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(UNAME_S),Darwin)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="make">  <span class="nv" style="color: #008080;">nproc</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> sysctl <span class="nt" style="color: #000080;">-n</span> hw.physicalcpu<span class="nv" style="color: #008080;">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">## all         : default task</span></span>

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -120,11 +114,11 @@ format: autopep8</td>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">## pylint      : run static code analysis on Python code</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="make"><span class="nl">pylint</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(PYSOURCES)</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="make"> pylint <span class="nt" style="color: #000080;">--msg-template</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}"</span> <span class="se" style="color: #d14;">\</span></span>

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<td class="diff-line-num old old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="make">                <span class="nv" style="color: #008080;">$^</span> <span class="nt" style="color: #000080;">-j</span><span class="nv" style="color: #008080;"><span class="idiff left right">$(nproc)</span></span><span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">true</span></span>

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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="make">                <span class="nv" style="color: #008080;">$^</span> <span class="nt" style="color: #000080;">-j<span class="idiff left right">0</span></span><span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">true</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="make"></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="make"><span class="nl">pylint_report.txt</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">${PYSOURCES}</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="make"> pylint <span class="nt" style="color: #000080;">--msg-template</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}"</span> <span class="se" style="color: #d14;">\</span></span>

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<td class="diff-line-num old old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="make">         <span class="nv" style="color: #008080;">$^</span> <span class="nt" style="color: #000080;">-j</span><span class="nv" style="color: #008080;"><span class="idiff left right">$(nproc)</span></span><span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$@</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">true</span></span>

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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="make">         <span class="nv" style="color: #008080;">$^</span> <span class="nt" style="color: #000080;">-j<span class="idiff left right">0</span></span><span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$@</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">true</span></span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="make"></span>

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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="make"><span class="nl">diff_pylint_report</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">pylint_report.txt</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="make"> diff-quality <span class="nt" style="color: #000080;">--violations</span><span class="o" style="font-weight: 600;">=</span>pylint pylint_report.txt</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -154,11 +148,11 @@ diff-cover.html:  coverage.xml</td>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="make"></span>

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<td class="diff-line-num new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">## test        : run the ${MODULE} test suite</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="make"><span class="nl">test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(pysources)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

157

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<td class="diff-line-num new_line old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC157" class="line" lang="make"> python setup.py <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">--addopts</span> <span class="s2" style="color: #d14;">"-n</span><span class="nv" style="color: #008080;"><span class="idiff left right">$(nproc)</span></span><span class="s2" style="color: #d14;"> --dist=loadfile"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="make"> python setup.py <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">--addopts</span> <span class="s2" style="color: #d14;">"-n<span class="idiff left right"> auto</span> --dist=loadfile"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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<td class="diff-line-num new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

152

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC152" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

159

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<td class="diff-line-num new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

153

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">## testcov     : run the ${MODULE} test suite and collect coverage</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

160

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<td class="diff-line-num new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

154

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC154" class="line" lang="make"><span class="nl">testcov</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(pysources)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

161

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<td class="diff-line-num new_line old" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC161" class="line" lang="make"> python setup.py <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">--addopts</span> <span class="s2" style="color: #d14;">"--cov cwltool -n</span><span class="nv" style="color: #008080;"><span class="idiff left right">$(nproc)</span></span><span class="s2" style="color: #d14;"> --dist=loadfile"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

155

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="make"> python setup.py <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">--addopts</span> <span class="s2" style="color: #d14;">"--cov cwltool -n<span class="idiff left right"> auto</span> --dist=loadfile"</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

162

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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

156

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC156" class="line" lang="make"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

163

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<td class="diff-line-num new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

157

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="make"><span class="nl">sloccount.sc</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">${PYSOURCES} Makefile</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

164

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<td class="diff-line-num new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="make"> sloccount <span class="nt" style="color: #000080;">--duplicates</span> <span class="nt" style="color: #000080;">--wide</span> <span class="nt" style="color: #000080;">--details</span> <span class="nv" style="color: #008080;">$^</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$@</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">Metadata</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">2.1</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"><span class="n" style="color: #333;">Name</span><span class="p">:</span> <span class="n" style="color: #333;">cwltool</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

</td>

<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">1.0.20190<span class="idiff left right">815141648</span></span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">1.0.20190<span class="idiff left right">915164430</span></span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"><span class="n" style="color: #333;">Summary</span><span class="p">:</span> <span class="n" style="color: #333;">Common</span> <span class="n" style="color: #333;">workflow</span> <span class="n" style="color: #333;">language</span> <span class="n" style="color: #333;">reference</span> <span class="n" style="color: #333;">implementation</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

</td>

<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">Home</span><span class="p">-</span><span class="n" style="color: #333;">page</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">Author</span><span class="p">:</span> <span class="n" style="color: #333;">Common</span> <span class="n" style="color: #333;">workflow</span> <span class="n" style="color: #333;">language</span> <span class="n" style="color: #333;">working</span> <span class="n" style="color: #333;">group</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,6 +13,10 @@ Description: ==================================================================</td>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel">        <span class="n" style="color: #333;">CWL</span> <span class="n" style="color: #333;">conformance</span> <span class="n" style="color: #333;">tests</span><span class="p">:</span> <span class="p">|</span><span class="n" style="color: #333;">Conformance</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Linux</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Windows</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Coverage</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Downloads</span><span class="p">|</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel">        <span class="p">|</span><span class="n" style="color: #333;">CommandLineTool</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">DockerRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">EnvVarRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">ExpressionTool</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel">        <span class="p">|</span><span class="n" style="color: #333;">InitialWorkDirRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">InlineJavascriptRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">MultipleInputRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Core</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="mosel">        <span class="p">|</span><span class="n" style="color: #333;">ResourceRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">ScatterRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">SchemaDefRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">ShellCommandequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="mosel">        <span class="p">|</span><span class="n" style="color: #333;">StepInputRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">SubWorkflowRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Workflow</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">Conformance</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">buildStatus</span><span class="p">/</span><span class="n" style="color: #333;">icon</span><span class="p">?</span><span class="n" style="color: #333;">job</span><span class="p">=</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,6 +33,52 @@ Description: ==================================================================</td>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">Downloads</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">pepy</span><span class="p">.</span><span class="n" style="color: #333;">tech</span><span class="p">/</span><span class="n" style="color: #333;">badge</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">month</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">pepy</span><span class="p">.</span><span class="n" style="color: #333;">tech</span><span class="p">/</span><span class="n" style="color: #333;">project</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span></span>

</pre>

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31

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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">CommandLineTool</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">command_line_tool</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">DockerRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">docker</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">EnvVarRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">env_var</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">ExpressionTool</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">expression_tool</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

46

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

47

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC47" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">InitialWorkDirRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">initial_work_dir</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

49

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

50

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

51

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">InlineJavascriptRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">inline_javascript</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

52

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

53

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

54

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">MultipleInputRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">multiple_input</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

55

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

56

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">Core</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">required</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

58

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

59

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC59" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">ResourceRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">resource</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

61

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

62

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

63

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">ScatterRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">scatter</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

64

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

65

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

66

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">SchemaDefRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">schema_def</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

67

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">ShellCommandequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">shell_command</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

70

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC71" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">StepInputRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">step_input</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

73

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

74

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">SubWorkflowRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">subworkflow</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

78

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">Workflow</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

80

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC80" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC81" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

32

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<td class="diff-line-num new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

82

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="mosel">        <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">reference</span> <span class="n" style="color: #333;">implementation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Common</span> <span class="n" style="color: #333;">Workflow</span> <span class="n" style="color: #333;">Language</span><span class="p">.</span>  <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">is</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

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<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

83

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC83" class="line" lang="mosel">        <span class="n" style="color: #333;">intended</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">feature</span> <span class="n" style="color: #333;">complete</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">provide</span> <span class="n" style="color: #333;">comprehensive</span> <span class="n" style="color: #333;">validation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">CWL</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

84

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC84" class="line" lang="mosel">        <span class="n" style="color: #333;">files</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">provide</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">tools</span> <span class="n" style="color: #333;">related</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">working</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">CWL</span><span class="p">.</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -53,15 +103,9 @@ Description: ==================================================================</td>

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<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="mosel">        </span>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="mosel">          <span class="n" style="color: #333;">apt</span><span class="p">-</span><span class="n" style="color: #333;">get</span> <span class="n" style="color: #333;">install</span> <span class="n" style="color: #333;">cwltool</span></span>

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<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="mosel">        </span>

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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="mosel">        <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">MacOS</span> <span class="n" style="color: #333;">X</span><span class="p">,</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">UNIXes</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">Windows</span> <span class="n" style="color: #333;">packages</span> <span class="n" style="color: #333;">prepared</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Bioconda</span> <span class="n" style="color: #333;">project</span><span class="p">.</span> <span class="n" style="color: #333;">Please</span> <span class="n" style="color: #333;">follow</span> <span class="n" style="color: #333;">instructions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Bioconda</span> <span class="p">(</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">bioconda</span><span class="p">.</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">io</span><span class="p">/)</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">installation</span><span class="p">,</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">perform</span><span class="p">:</span> </span>

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<td class="diff-line-num old old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="mosel">        </span>

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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="mosel">        <span class="p">..</span> <span class="n" style="color: #333;">code</span><span class="p">::</span> <span class="n" style="color: #333;">bash</span></span>

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<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="mosel">        </span>

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<td class="diff-line-num old old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="mosel">          <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">install</span> <span class="p">-</span><span class="n" style="color: #333;">c</span> <span class="n" style="color: #333;">bioconda</span> <span class="n" style="color: #333;">cwltool</span> </span>

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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="mosel">        </span>

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<td class="diff-line-num old old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="mosel">        <span class="n" style="color: #333;">Under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">hood</span><span class="p">,</span> <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">setups</span> <span class="n" style="color: #333;">virtual</span> <span class="n" style="color: #333;">environments</span> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">installing</span> <span class="p">`</span><span class="n" style="color: #333;">cwltool</span><span class="p">`</span> <span class="k" style="font-weight: 600;">to</span></span>

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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="mosel">        <span class="n" style="color: #333;">avoid</span> <span class="n" style="color: #333;">conflicting</span> <span class="n" style="color: #333;">versions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">library</span><span class="p">.</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">installing</span> <span class="n" style="color: #333;">cwltool</span> <span class="n" style="color: #333;">directly</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="mosel">        <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">recommended</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">manually</span><span class="p">:</span></span>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="mosel">        <span class="n" style="color: #333;">Otherwise</span><span class="p">,</span> <span class="k" style="font-weight: 600;">to</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="mosel">        <span class="n" style="color: #333;">avoid</span> <span class="n" style="color: #333;">conflicting</span> <span class="n" style="color: #333;">versions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">library</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="mosel">        <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">recommended</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="mosel">        </span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="mosel">        <span class="p">..</span> <span class="n" style="color: #333;">code</span><span class="p">::</span> <span class="n" style="color: #333;">bash</span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="mosel">        </span>

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<br>

</li>

<li id="561b88e19de321ca62c7590bbb350765fb110905">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,10 @@ Common Workflow Language tool description reference implementation</td>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">CWL</span> <span class="n" style="color: #333;">conformance</span> <span class="n" style="color: #333;">tests</span><span class="p">:</span> <span class="p">|</span><span class="n" style="color: #333;">Conformance</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Linux</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Windows</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Coverage</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Downloads</span><span class="p">|</span></span>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"></span>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"><span class="p">|</span><span class="n" style="color: #333;">CommandLineTool</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">DockerRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">EnvVarRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">ExpressionTool</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> </span>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="p">|</span><span class="n" style="color: #333;">InitialWorkDirRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">InlineJavascriptRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">MultipleInputRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Core</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span></span>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"><span class="p">|</span><span class="n" style="color: #333;">ResourceRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">ScatterRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">SchemaDefRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">ShellCommandequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"><span class="p">|</span><span class="n" style="color: #333;">StepInputRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">SubWorkflowRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Workflow</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"></span>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">Conformance</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">buildStatus</span><span class="p">/</span><span class="n" style="color: #333;">icon</span><span class="p">?</span><span class="n" style="color: #333;">job</span><span class="p">=</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,6 +24,52 @@ CWL conformance tests: |Conformance Status| |Linux Status| |Windows Status| |Cov</td>

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">Downloads</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">pepy</span><span class="p">.</span><span class="n" style="color: #333;">tech</span><span class="p">/</span><span class="n" style="color: #333;">badge</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">month</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">pepy</span><span class="p">.</span><span class="n" style="color: #333;">tech</span><span class="p">/</span><span class="n" style="color: #333;">project</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC26" class="line" lang="mosel"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">CommandLineTool</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">command_line_tool</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="mosel"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">DockerRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">docker</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

31

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="mosel"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">EnvVarRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">env_var</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

34

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC34" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="mosel"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">ExpressionTool</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">expression_tool</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC38" class="line" lang="mosel"></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

39

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">InitialWorkDirRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">initial_work_dir</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

40

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC41" class="line" lang="mosel"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

42

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">InlineJavascriptRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">inline_javascript</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

43

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

44

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

45

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">MultipleInputRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">multiple_input</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

46

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

47

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC47" class="line" lang="mosel"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

48

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC48" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">Core</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">required</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

49

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

50

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel"></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

51

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">ResourceRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">resource</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

52

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

53

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

54

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">ScatterRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">scatter</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

55

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

56

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC56" class="line" lang="mosel"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

57

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC57" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">SchemaDefRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">schema_def</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

58

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC58" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

59

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC59" class="line" lang="mosel"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

60

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC60" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">ShellCommandequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">shell_command</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

62

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC62" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

63

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">StepInputRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">step_input</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

64

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

65

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC65" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

66

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC66" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">SubWorkflowRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">subworkflow</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

67

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

68

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC68" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

69

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC69" class="line" lang="mosel"><span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">Workflow</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

70

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC70" class="line" lang="mosel">   <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC71" class="line" lang="mosel"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC72" class="line" lang="mosel"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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<td class="diff-line-num new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">reference</span> <span class="n" style="color: #333;">implementation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Common</span> <span class="n" style="color: #333;">Workflow</span> <span class="n" style="color: #333;">Language</span><span class="p">.</span>  <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">is</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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<td class="diff-line-num new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="mosel"><span class="n" style="color: #333;">intended</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">feature</span> <span class="n" style="color: #333;">complete</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">provide</span> <span class="n" style="color: #333;">comprehensive</span> <span class="n" style="color: #333;">validation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">CWL</span></span>

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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="mosel"><span class="n" style="color: #333;">files</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">provide</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">tools</span> <span class="n" style="color: #333;">related</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">working</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">CWL</span><span class="p">.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,15 +94,9 @@ Your operating system may offer cwltool directly. For [Debian](https://tracker.d</td>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="mosel"></span>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="mosel">  <span class="n" style="color: #333;">apt</span><span class="p">-</span><span class="n" style="color: #333;">get</span> <span class="n" style="color: #333;">install</span> <span class="n" style="color: #333;">cwltool</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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<td class="diff-line-num new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="mosel"><span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">MacOS</span> <span class="n" style="color: #333;">X</span><span class="p">,</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">UNIXes</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">Windows</span> <span class="n" style="color: #333;">packages</span> <span class="n" style="color: #333;">prepared</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Bioconda</span> <span class="n" style="color: #333;">project</span><span class="p">.</span> <span class="n" style="color: #333;">Please</span> <span class="n" style="color: #333;">follow</span> <span class="n" style="color: #333;">instructions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Bioconda</span> <span class="p">(</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">bioconda</span><span class="p">.</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">io</span><span class="p">/)</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">installation</span><span class="p">,</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">perform</span><span class="p">:</span> </span>

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<td class="diff-line-num new_line old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="mosel"><span class="p">..</span> <span class="n" style="color: #333;">code</span><span class="p">::</span> <span class="n" style="color: #333;">bash</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="mosel">  <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">install</span> <span class="p">-</span><span class="n" style="color: #333;">c</span> <span class="n" style="color: #333;">bioconda</span> <span class="n" style="color: #333;">cwltool</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="mosel"><span class="n" style="color: #333;">Under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">hood</span><span class="p">,</span> <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">setups</span> <span class="n" style="color: #333;">virtual</span> <span class="n" style="color: #333;">environments</span> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">installing</span> <span class="p">`</span><span class="n" style="color: #333;">cwltool</span><span class="p">`</span> <span class="k" style="font-weight: 600;">to</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="mosel"><span class="n" style="color: #333;">avoid</span> <span class="n" style="color: #333;">conflicting</span> <span class="n" style="color: #333;">versions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">library</span><span class="p">.</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">installing</span> <span class="n" style="color: #333;">cwltool</span> <span class="n" style="color: #333;">directly</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="mosel"><span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">recommended</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">manually</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="mosel"><span class="n" style="color: #333;">Otherwise</span><span class="p">,</span> <span class="k" style="font-weight: 600;">to</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="mosel"><span class="n" style="color: #333;">avoid</span> <span class="n" style="color: #333;">conflicting</span> <span class="n" style="color: #333;">versions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">library</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

99

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="mosel"><span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">recommended</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

56

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<td class="diff-line-num new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

57

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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

101

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="mosel"><span class="p">..</span> <span class="n" style="color: #333;">code</span><span class="p">::</span> <span class="n" style="color: #333;">bash</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

58

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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

102

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="mosel"></span>

</pre>

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<br>

</li>

<li id="b56b7a64ee5cdb86aa33e58c869fc85468a88dfe">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#b56b7a64ee5cdb86aa33e58c869fc85468a88dfe"><strong>cwltool.egg-info/PKG-INFO</strong></a>

<hr>

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<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">Metadata</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">2.1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"><span class="n" style="color: #333;">Name</span><span class="p">:</span> <span class="n" style="color: #333;">cwltool</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">1.0.20190<span class="idiff left right">815141648</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">1.0.20190<span class="idiff left right">915164430</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"><span class="n" style="color: #333;">Summary</span><span class="p">:</span> <span class="n" style="color: #333;">Common</span> <span class="n" style="color: #333;">workflow</span> <span class="n" style="color: #333;">language</span> <span class="n" style="color: #333;">reference</span> <span class="n" style="color: #333;">implementation</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">Home</span><span class="p">-</span><span class="n" style="color: #333;">page</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">Author</span><span class="p">:</span> <span class="n" style="color: #333;">Common</span> <span class="n" style="color: #333;">workflow</span> <span class="n" style="color: #333;">language</span> <span class="n" style="color: #333;">working</span> <span class="n" style="color: #333;">group</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,6 +13,10 @@ Description: ==================================================================</td>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel">        <span class="n" style="color: #333;">CWL</span> <span class="n" style="color: #333;">conformance</span> <span class="n" style="color: #333;">tests</span><span class="p">:</span> <span class="p">|</span><span class="n" style="color: #333;">Conformance</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Linux</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Windows</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Coverage</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Downloads</span><span class="p">|</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel">        <span class="p">|</span><span class="n" style="color: #333;">CommandLineTool</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">DockerRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">EnvVarRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">ExpressionTool</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel">        <span class="p">|</span><span class="n" style="color: #333;">InitialWorkDirRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">InlineJavascriptRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">MultipleInputRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Core</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="mosel">        <span class="p">|</span><span class="n" style="color: #333;">ResourceRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">ScatterRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">SchemaDefRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">ShellCommandequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="mosel">        <span class="p">|</span><span class="n" style="color: #333;">StepInputRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">SubWorkflowRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="p">|</span><span class="n" style="color: #333;">Workflow</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">Conformance</span> <span class="n" style="color: #333;">Status</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">buildStatus</span><span class="p">/</span><span class="n" style="color: #333;">icon</span><span class="p">?</span><span class="n" style="color: #333;">job</span><span class="p">=</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,6 +33,52 @@ Description: ==================================================================</td>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">Downloads</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">pepy</span><span class="p">.</span><span class="n" style="color: #333;">tech</span><span class="p">/</span><span class="n" style="color: #333;">badge</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">month</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

30

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">pepy</span><span class="p">.</span><span class="n" style="color: #333;">tech</span><span class="p">/</span><span class="n" style="color: #333;">project</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">CommandLineTool</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">command_line_tool</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">DockerRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">docker</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

42

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">EnvVarRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">env_var</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

43

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

44

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel">        </span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

45

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">ExpressionTool</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">expression_tool</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

46

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

47

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC47" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">InitialWorkDirRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">initial_work_dir</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

49

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

50

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel">        </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

51

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">InlineJavascriptRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">inline_javascript</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

54

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">MultipleInputRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">multiple_input</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

55

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

56

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

57

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">Core</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">required</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

58

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

59

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">ResourceRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">resource</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

61

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">ScatterRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">scatter</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

65

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

66

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">SchemaDefRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">schema_def</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

67

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">ShellCommandequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">shell_command</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

70

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">StepInputRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">step_input</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

73

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

74

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">SubWorkflowRequirement</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">subworkflow</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="mosel">        <span class="p">..</span> <span class="p">|</span><span class="n" style="color: #333;">Workflow</span> <span class="n" style="color: #333;">Support</span><span class="p">|</span> <span class="n" style="color: #333;">image</span><span class="p">::</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">flat</span><span class="p">.</span><span class="n" style="color: #333;">badgen</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">https</span><span class="p">/</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">githubusercontent</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">common</span><span class="p">-</span><span class="n" style="color: #333;">workflow</span><span class="p">-</span><span class="n" style="color: #333;">language</span><span class="p">/</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span><span class="n" style="color: #333;">master</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">/</span><span class="n" style="color: #333;">cwl_v1</span><span class="m" style="color: #099;">.0</span><span class="p">/</span><span class="n" style="color: #333;">cwltool_latest</span><span class="p">/</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">json</span></span>

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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="mosel">           <span class="p">:</span><span class="n" style="color: #333;">target</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">ci</span><span class="p">.</span><span class="n" style="color: #333;">commonwl</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">job</span><span class="p">/</span><span class="n" style="color: #333;">cwltool</span><span class="p">-</span><span class="n" style="color: #333;">conformance</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="mosel">        <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">reference</span> <span class="n" style="color: #333;">implementation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Common</span> <span class="n" style="color: #333;">Workflow</span> <span class="n" style="color: #333;">Language</span><span class="p">.</span>  <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">is</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="mosel">        <span class="n" style="color: #333;">intended</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">feature</span> <span class="n" style="color: #333;">complete</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">provide</span> <span class="n" style="color: #333;">comprehensive</span> <span class="n" style="color: #333;">validation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">CWL</span></span>

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<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="mosel">        <span class="n" style="color: #333;">files</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">provide</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">tools</span> <span class="n" style="color: #333;">related</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">working</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">CWL</span><span class="p">.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -53,15 +103,9 @@ Description: ==================================================================</td>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="mosel">        </span>

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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="mosel">          <span class="n" style="color: #333;">apt</span><span class="p">-</span><span class="n" style="color: #333;">get</span> <span class="n" style="color: #333;">install</span> <span class="n" style="color: #333;">cwltool</span></span>

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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="mosel">        </span>

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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="mosel">        <span class="n" style="color: #333;">For</span> <span class="n" style="color: #333;">MacOS</span> <span class="n" style="color: #333;">X</span><span class="p">,</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">UNIXes</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">Windows</span> <span class="n" style="color: #333;">packages</span> <span class="n" style="color: #333;">prepared</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Bioconda</span> <span class="n" style="color: #333;">project</span><span class="p">.</span> <span class="n" style="color: #333;">Please</span> <span class="n" style="color: #333;">follow</span> <span class="n" style="color: #333;">instructions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Bioconda</span> <span class="p">(</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">bioconda</span><span class="p">.</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">io</span><span class="p">/)</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">installation</span><span class="p">,</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">perform</span><span class="p">:</span> </span>

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="mosel">        </span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="mosel">        <span class="p">..</span> <span class="n" style="color: #333;">code</span><span class="p">::</span> <span class="n" style="color: #333;">bash</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

59

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

60

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="mosel">          <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">install</span> <span class="p">-</span><span class="n" style="color: #333;">c</span> <span class="n" style="color: #333;">bioconda</span> <span class="n" style="color: #333;">cwltool</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

61

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

62

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="mosel">        <span class="n" style="color: #333;">Under</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">hood</span><span class="p">,</span> <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">setups</span> <span class="n" style="color: #333;">virtual</span> <span class="n" style="color: #333;">environments</span> <span class="n" style="color: #333;">before</span> <span class="n" style="color: #333;">installing</span> <span class="p">`</span><span class="n" style="color: #333;">cwltool</span><span class="p">`</span> <span class="k" style="font-weight: 600;">to</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

63

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="mosel">        <span class="n" style="color: #333;">avoid</span> <span class="n" style="color: #333;">conflicting</span> <span class="n" style="color: #333;">versions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">library</span><span class="p">.</span> <span class="n" style="color: #333;">When</span> <span class="n" style="color: #333;">installing</span> <span class="n" style="color: #333;">cwltool</span> <span class="n" style="color: #333;">directly</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

64

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="mosel">        <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">recommended</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">manually</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="mosel">        <span class="n" style="color: #333;">Otherwise</span><span class="p">,</span> <span class="k" style="font-weight: 600;">to</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC107" class="line" lang="mosel">        <span class="n" style="color: #333;">avoid</span> <span class="n" style="color: #333;">conflicting</span> <span class="n" style="color: #333;">versions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">library</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

108

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="mosel">        <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">recommended</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="mosel">        </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="mosel">        <span class="p">..</span> <span class="n" style="color: #333;">code</span><span class="p">::</span> <span class="n" style="color: #333;">bash</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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<td class="diff-line-num new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="mosel">        </span>

</pre>

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<br>

</li>

<li id="0f5f9a487de6f81f4140b1291f27031478a7b0b2">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#0f5f9a487de6f81f4140b1291f27031478a7b0b2"><strong>cwltool.egg-info/SOURCES.txt</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -178,6 +178,7 @@ cwltool/schemas/v1.1/salad/schema_salad/metaschema/vocab_res_src.yml</td>

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<td class="diff-line-num old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

178

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<td class="diff-line-num new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

178

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext">tests/2.fasta</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext">tests/2.fastq</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

180

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<td class="diff-line-num new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

180

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="plaintext">tests/__init__.py</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

181

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">tests/arg-empty-prefix-separate-false.cwl</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

181

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<td class="diff-line-num new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

182

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext">tests/bundle-context.jsonld</span>

</pre>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="plaintext">tests/debian_image_id.cwl</span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="plaintext">tests/echo-job.yaml</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -186,6 +187,7 @@ tests/echo-position-expr.cwl</td>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="plaintext">tests/echo.cwl</span>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="plaintext">tests/echo_broken_outputs.cwl</span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="plaintext">tests/env.cwl</span>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">tests/env2.cwl</span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="plaintext">tests/listing-job.yml</span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="plaintext">tests/listing2-job.yml</span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="plaintext">tests/non_portable.cwl</span>

</pre>

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<br>

</li>

<li id="f37416a929e52b34959bfb17948722683d25dca6">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#f37416a929e52b34959bfb17948722683d25dca6"><strong>cwltool/argparser.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -394,14 +394,16 @@ class DirectoryAppendAction(FSAppendAction):</td>

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">toolparser</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">inptype</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span></span>

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<td class="diff-line-num new_line old" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python">                 <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

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<td class="diff-line-num old old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># type: (argparse.ArgumentParser, Text, Any, List[Text], Text, Any) -> None</span></span>

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python">                 <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">input_required</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># type: (argparse.ArgumentParser, Text, Any, List[Text], Text, Any<span class="idiff left right">, bool</span>) -> None</span></span>

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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python">        <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span></span>

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="python">        <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"--"</span></span>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python">    <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># if input_required is false, don't make the command line</span></span>

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># parameter required.</span></span>

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python">    <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">input_required</span></span>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">inptype</span><span class="p">,</span> <span class="n" style="color: #333;">MutableSequence</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">inptype</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"null"</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python">            <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -462,8 +464,8 @@ def add_argument(toolparser, name, inptype, records, description="",</td>

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python">        <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">typekw</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC465" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_parser</span><span class="p">(</span><span class="n" style="color: #333;">toolparser</span><span class="p">,</span> <span class="n" style="color: #333;">tool</span><span class="p">,</span> <span class="n" style="color: #333;">namemap</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC466" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># type: (argparse.ArgumentParser, Process, Dict[Text, Text], List[Text]) -> argparse.ArgumentParser</span></span>

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_parser</span><span class="p">(</span><span class="n" style="color: #333;">toolparser</span><span class="p">,</span> <span class="n" style="color: #333;">tool</span><span class="p">,</span> <span class="n" style="color: #333;">namemap</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">input_required</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># type: (argparse.ArgumentParser, Process, Dict[Text, Text], List[Text]<span class="idiff left right">, bool</span>) -> argparse.ArgumentParser</span></span>

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="python">    <span class="n" style="color: #333;">toolparser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"job_order"</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"?"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Job input json file"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="python">    <span class="n" style="color: #333;">namemap</span><span class="p">[</span><span class="s" style="color: #d14;">"job_order"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"job_order"</span></span>

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -473,6 +475,6 @@ def generate_parser(toolparser, tool, namemap, records):</td>

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="python">        <span class="n" style="color: #333;">inptype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inp</span><span class="p">[</span><span class="s" style="color: #d14;">"type"</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="python">        <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"doc"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="python">        <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"default"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC476" class="line" lang="python">        <span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">toolparser</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">inptype</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python">        <span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">toolparser</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">inptype</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">input_required</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">toolparser</span></span></pre>

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<br>

</li>

<li id="157096f5f986f141b1bd83003c5b5ce452ecd020">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#157096f5f986f141b1bd83003c5b5ce452ecd020"><strong>cwltool/builder.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -426,7 +426,7 @@ class Builder(HasReqsHints):</td>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sep</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python">                <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tostr</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">)])</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="diff-line-num new_line old" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC429" class="line" lang="python">                <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">""</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">prefix</span></span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tostr</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python">                <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tostr</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">prefix</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">is</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tostr</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"></span>

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<br>

</li>

<li id="255ee49f33c79c25f6a55971fe53bd72a9fb8575">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#255ee49f33c79c25f6a55971fe53bd72a9fb8575"><strong>cwltool/executors.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -159,7 +159,8 @@ class SingleJobExecutor(JobExecutor):</td>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python">                <span class="n" style="color: #333;">user_provenance</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python">                <span class="n" style="color: #333;">orcid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">runtime_context</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orcid</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># single tool execution, so RO UUID = wf UUID = tool UUID</span></span>

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python">                <span class="n" style="color: #333;">run_uuid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">runtime_context</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ro_uuid</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python">                <span class="n" style="color: #333;">run_uuid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">runtime_context</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ro_uuid</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python">                <span class="n" style="color: #333;">fsaccess</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">runtime_context</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">make_fs_access</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python">            <span class="n" style="color: #333;">process</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent_wf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">provenance_object</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python">        <span class="n" style="color: #333;">jobiter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">job</span><span class="p">(</span><span class="n" style="color: #333;">job_order_object</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output_callback</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python">                              <span class="n" style="color: #333;">runtime_context</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -178,6 +179,7 @@ class SingleJobExecutor(JobExecutor):</td>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python">                            <span class="n" style="color: #333;">prov_obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">job</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prov_obj</span></span>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prov_obj</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python">                            <span class="n" style="color: #333;">runtime_context</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prov_obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prov_obj</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python">                            <span class="n" style="color: #333;">prov_obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fsaccess</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runtime_context</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">make_fs_access</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>

</pre>

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181

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python">                            <span class="n" style="color: #333;">prov_obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">evaluate</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python">                                <span class="n" style="color: #333;">process</span><span class="p">,</span> <span class="n" style="color: #333;">job</span><span class="p">,</span> <span class="n" style="color: #333;">job_order_object</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python">                                <span class="n" style="color: #333;">runtime_context</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_obj</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="1a4debaa3574d5d928e4fc1d259929cac851b4b6">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#1a4debaa3574d5d928e4fc1d259929cac851b4b6"><strong>cwltool/job.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -621,6 +621,16 @@ class ContainerCommandLineJob(with_metaclass(ABCMeta, JobBase)):</td>

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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python">                <span class="n" style="color: #333;">img_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">docker_req</span><span class="p">[</span><span class="s" style="color: #d14;">"dockerImageId"</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'dockerPull'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">docker_req</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python">                <span class="n" style="color: #333;">img_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">docker_req</span><span class="p">[</span><span class="s" style="color: #d14;">"dockerPull"</span><span class="p">])</span></span>

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<pre style="margin: 0;">+<span id="LC624" class="line" lang="python">                <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">user_space_docker_cmd</span><span class="p">,</span> <span class="s" style="color: #d14;">"pull"</span><span class="p">,</span> <span class="n" style="color: #333;">img_id</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC625" class="line" lang="python">                <span class="n" style="color: #333;">_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="n" style="color: #333;">Text</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC626" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC627" class="line" lang="python">                    <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC629" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowException</span><span class="p">(</span><span class="n" style="color: #333;">SourceLine</span><span class="p">(</span><span class="n" style="color: #333;">docker_req</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">makeError</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC630" class="line" lang="python">                        <span class="s" style="color: #d14;">"Either Docker container {} is not available with "</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC631" class="line" lang="python">                        <span class="s" style="color: #d14;">"user space docker implementation {} or {} is missing "</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

632

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<pre style="margin: 0;">+<span id="LC632" class="line" lang="python">                        <span class="s" style="color: #d14;">"or broken."</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">img_id</span><span class="p">,</span> <span class="n" style="color: #333;">user_space_docker_cmd</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

633

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<pre style="margin: 0;">+<span id="LC633" class="line" lang="python">                                            <span class="n" style="color: #333;">user_space_docker_cmd</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

624

</td>

<td class="diff-line-num new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

634

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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

625

</td>

<td class="diff-line-num new_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

635

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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowException</span><span class="p">(</span><span class="n" style="color: #333;">SourceLine</span><span class="p">(</span><span class="n" style="color: #333;">docker_req</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">makeError</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

626

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<td class="diff-line-num new_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

636

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<pre style="margin: 0;"> <span id="LC636" class="line" lang="python">                    <span class="s" style="color: #d14;">"Docker image must be specified as 'dockerImageId' or "</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -695,8 +705,11 @@ class ContainerCommandLineJob(with_metaclass(ABCMeta, JobBase)):</td>

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<td class="diff-line-num old_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

695

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<td class="diff-line-num new_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

705

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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python">            <span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sleep</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

696

</td>

<td class="diff-line-num new_line" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

706

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<pre style="margin: 0;"> <span id="LC706" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">process</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">returncode</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

697

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<td class="diff-line-num new_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

707

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<pre style="margin: 0;"> <span id="LC707" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cleanup_cidfile</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

698

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<td class="diff-line-num new_line old" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC698" class="line" lang="python">                    <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">cidfile</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

699

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<td class="diff-line-num new_line old" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC699" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

708

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC708" class="line" lang="python">                    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

709

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC709" class="line" lang="python">                        <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">cidfile</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

710

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC710" class="line" lang="python">                    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">exc</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

711

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC711" class="line" lang="python">                        <span class="n" style="color: #333;">_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Ignored error cleaning up Docker cidfile: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span><span class="p">,</span> <span class="n" style="color: #333;">exc</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

712

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC712" class="line" lang="python">                    <span class="k" style="font-weight: 600;">return</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

700

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<td class="diff-line-num new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC713" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

701

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<td class="diff-line-num new_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

714

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC714" class="line" lang="python">                <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">cidfile</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">cidhandle</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python">                    <span class="n" style="color: #333;">cid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cidhandle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readline</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -705,12 +718,16 @@ class ContainerCommandLineJob(with_metaclass(ABCMeta, JobBase)):</td>

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<td class="diff-line-num old_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python">        <span class="n" style="color: #333;">max_mem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">psutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">virtual_memory</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">total</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC719" class="line" lang="python">        <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir_prefix</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

707

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<td class="diff-line-num new_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC720" class="line" lang="python">        <span class="n" style="color: #333;">stats_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tmp_prefix</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC708" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">stats_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">stats_file_handle</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC709" class="line" lang="python">            <span class="n" style="color: #333;">stats_proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

710

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<td class="diff-line-num new_line old" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC710" class="line" lang="python">                <span class="p">[</span><span class="s" style="color: #d14;">'docker'</span><span class="p">,</span> <span class="s" style="color: #d14;">'stats'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--no-trunc'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--format'</span><span class="p">,</span> <span class="s" style="color: #d14;">'{{.MemPerc}}'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

711

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<td class="diff-line-num new_line old" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC711" class="line" lang="python">                 <span class="n" style="color: #333;">cid</span><span class="p">],</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stats_file_handle</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DEVNULL</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC712" class="line" lang="python">            <span class="n" style="color: #333;">process</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wait</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC713" class="line" lang="python">            <span class="n" style="color: #333;">stats_proc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kill</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

721

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<pre style="margin: 0;">+<span id="LC721" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

722

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<pre style="margin: 0;">+<span id="LC722" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">stats_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">stats_file_handle</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

723

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<pre style="margin: 0;">+<span id="LC723" class="line" lang="python">                <span class="n" style="color: #333;">stats_proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

724

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<pre style="margin: 0;">+<span id="LC724" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">'docker'</span><span class="p">,</span> <span class="s" style="color: #d14;">'stats'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--no-trunc'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--format'</span><span class="p">,</span> <span class="s" style="color: #d14;">'{{.MemPerc}}'</span><span class="p">,</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

725

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<pre style="margin: 0;">+<span id="LC725" class="line" lang="python">                     <span class="n" style="color: #333;">cid</span><span class="p">],</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stats_file_handle</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DEVNULL</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC726" class="line" lang="python">                <span class="n" style="color: #333;">process</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wait</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC727" class="line" lang="python">                <span class="n" style="color: #333;">stats_proc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kill</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC728" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">exc</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC729" class="line" lang="python">            <span class="n" style="color: #333;">_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Ignored error with docker stats: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span><span class="p">,</span> <span class="n" style="color: #333;">exc</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC730" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span></span>

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<pre style="margin: 0;"> <span id="LC731" class="line" lang="python">        <span class="n" style="color: #333;">max_mem_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC732" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">stats_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">stats</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC733" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">stats</span><span class="p">:</span></span>

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<br>

</li>

<li id="ef56fd169f82fcdcb5c4e7b80a7164f20004c766">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#ef56fd169f82fcdcb5c4e7b80a7164f20004c766"><strong>cwltool/main.py</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -285,14 +285,15 @@ def init_job_order(job_order_object,        # type: Optional[MutableMapping[Text</td>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python">                   <span class="n" style="color: #333;">relative_deps</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span>     <span class="c1" style="color: #998; font-style: italic;"># type: bool</span></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python">                   <span class="n" style="color: #333;">make_fs_access</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">StdFsAccess</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;"># type: Callable[[Text], StdFsAccess]</span></span>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python">                   <span class="n" style="color: #333;">input_basedir</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span>        <span class="c1" style="color: #998; font-style: italic;"># type: Text</span></span>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python">                   <span class="n" style="color: #333;">secret_store</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span>        <span class="c1" style="color: #998; font-style: italic;"># type: Optional[SecretStore]</span></span>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python">                   <span class="n" style="color: #333;">secret_store</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span>       <span class="c1" style="color: #998; font-style: italic;"># type: Optional[SecretStore]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python">                   <span class="n" style="color: #333;">input_required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span>      <span class="c1" style="color: #998; font-style: italic;"># type: bool</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python">                  <span class="p">):</span>  <span class="c1" style="color: #998; font-style: italic;"># type: (...) -> MutableMapping[Text, Any]</span></span>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python">    <span class="n" style="color: #333;">secrets_req</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_requirement</span><span class="p">(</span><span class="s" style="color: #d14;">"http://commonwl.org/cwltool#Secrets"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">job_order_object</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python">        <span class="n" style="color: #333;">namemap</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span>  <span class="c1" style="color: #998; font-style: italic;"># type: Dict[Text, Text]</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python">        <span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span>  <span class="c1" style="color: #998; font-style: italic;"># type: List[Text]</span></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python">        <span class="n" style="color: #333;">toolparser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">generate_parser</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python">            <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">prog</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">workflow</span><span class="p">),</span> <span class="n" style="color: #333;">process</span><span class="p">,</span> <span class="n" style="color: #333;">namemap</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python">            <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">prog</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">workflow</span><span class="p">),</span> <span class="n" style="color: #333;">process</span><span class="p">,</span> <span class="n" style="color: #333;">namemap</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">input_required</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tool_help</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python">            <span class="n" style="color: #333;">toolparser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">print_help</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python">            <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -490,7 +491,8 @@ def main(argsl=None,                   # type: Optional[List[str]]</td>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python">         <span class="n" style="color: #333;">custom_schema_callback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;"># type: Optional[Callable[[], None]]</span></span>

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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python">         <span class="n" style="color: #333;">executor</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span>                <span class="c1" style="color: #998; font-style: italic;"># type: Optional[JobExecutor]</span></span>

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python">         <span class="n" style="color: #333;">loadingContext</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span>          <span class="c1" style="color: #998; font-style: italic;"># type: Optional[LoadingContext]</span></span>

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<pre style="margin: 0;">-<span id="LC493" class="line" lang="python">         <span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span>           <span class="c1" style="color: #998; font-style: italic;"># type: Optional[RuntimeContext]</span></span>

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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python">         <span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span>          <span class="c1" style="color: #998; font-style: italic;"># type: Optional[RuntimeContext]</span></span>

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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python">         <span class="n" style="color: #333;">input_required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span>           <span class="c1" style="color: #998; font-style: italic;"># type: bool</span></span>

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="python">        <span class="p">):</span>  <span class="c1" style="color: #998; font-style: italic;"># type: (...) -> int</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

495

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<td class="diff-line-num new_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

497

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<pre style="margin: 0;"> <span id="LC497" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">stdout</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># force UTF-8 even if the console is configured differently</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

496

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<td class="diff-line-num new_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

498

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"encoding"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -598,6 +600,7 @@ def main(argsl=None,                   # type: Optional[List[str]]</td>

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<td class="diff-line-num old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

598

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<td class="diff-line-num new_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

600

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<pre style="margin: 0;"> <span id="LC600" class="line" lang="python">                <span class="n" style="color: #333;">_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"--provenance incompatible with --no-compute-checksum"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

599

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<td class="diff-line-num new_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

601

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<pre style="margin: 0;"> <span id="LC601" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

600

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<td class="diff-line-num new_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

602

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<pre style="margin: 0;"> <span id="LC602" class="line" lang="python">            <span class="n" style="color: #333;">ro</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ResearchObject</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

603

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<pre style="margin: 0;">+<span id="LC603" class="line" lang="python">                <span class="n" style="color: #333;">getdefault</span><span class="p">(</span><span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">make_fs_access</span><span class="p">,</span> <span class="n" style="color: #333;">StdFsAccess</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

601

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<td class="diff-line-num new_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

604

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<pre style="margin: 0;"> <span id="LC604" class="line" lang="python">                <span class="n" style="color: #333;">temp_prefix_ro</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tmpdir_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">orcid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orcid</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

602

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<td class="diff-line-num new_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

605

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<pre style="margin: 0;"> <span id="LC605" class="line" lang="python">                <span class="n" style="color: #333;">full_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cwl_full_name</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

603

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<td class="diff-line-num new_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

606

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<pre style="margin: 0;"> <span id="LC606" class="line" lang="python">            <span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ro</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -795,7 +798,8 @@ def main(argsl=None,                   # type: Optional[List[str]]</td>

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<td class="diff-line-num old_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

795

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<td class="diff-line-num new_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

798

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<pre style="margin: 0;"> <span id="LC798" class="line" lang="python">                <span class="n" style="color: #333;">relative_deps</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">relative_deps</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

796

</td>

<td class="diff-line-num new_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

799

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC799" class="line" lang="python">                <span class="n" style="color: #333;">make_fs_access</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">make_fs_access</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

797

</td>

<td class="diff-line-num new_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

800

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<pre style="margin: 0;"> <span id="LC800" class="line" lang="python">                <span class="n" style="color: #333;">input_basedir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_basedir</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

798

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<td class="diff-line-num new_line old" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC798" class="line" lang="python">                <span class="n" style="color: #333;">secret_store</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secret_store</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

801

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC801" class="line" lang="python">                <span class="n" style="color: #333;">secret_store</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secret_store</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

802

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC802" class="line" lang="python">                <span class="n" style="color: #333;">input_required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_required</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

799

</td>

<td class="diff-line-num new_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

803

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC803" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">SystemExit</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">err</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

800

</td>

<td class="diff-line-num new_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

804

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC804" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">code</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

801

</td>

<td class="diff-line-num new_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

805

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC805" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -833,6 +837,21 @@ def main(argsl=None,                   # type: Optional[List[str]]</td>

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<td class="diff-line-num old_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

833

</td>

<td class="diff-line-num new_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

837

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC837" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_obj</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

834

</td>

<td class="diff-line-num new_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

838

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC838" class="line" lang="python">                    <span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_job</span><span class="p">(</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

835

</td>

<td class="diff-line-num new_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

839

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC839" class="line" lang="python">                        <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

840

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC840" class="line" lang="python">                    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_at_id</span><span class="p">(</span><span class="n" style="color: #333;">doc</span><span class="p">):</span>  <span class="c1" style="color: #998; font-style: italic;"># type: (MutableMapping[Text, Any]) -> None</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

841

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC841" class="line" lang="python">                        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">()):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

842

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC842" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'@id'</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

843

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC843" class="line" lang="python">                                <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">doc</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

844

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC844" class="line" lang="python">                            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

845

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC845" class="line" lang="python">                                <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">doc</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

846

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC846" class="line" lang="python">                                <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">MutableMapping</span><span class="p">):</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

847

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC847" class="line" lang="python">                                    <span class="n" style="color: #333;">remove_at_id</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

848

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC848" class="line" lang="python">                                <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">MutableSequence</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

849

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC849" class="line" lang="python">                                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">entry</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">value</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

850

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC850" class="line" lang="python">                                        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">,</span> <span class="n" style="color: #333;">MutableMapping</span><span class="p">):</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC851" class="line" lang="python">                                            <span class="n" style="color: #333;">remove_at_id</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC852" class="line" lang="python">                    <span class="n" style="color: #333;">remove_at_id</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC853" class="line" lang="python">                    <span class="n" style="color: #333;">visit_class</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="p">(</span><span class="s" style="color: #d14;">"File"</span><span class="p">,),</span> <span class="n" style="color: #333;">functools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">partial</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC854" class="line" lang="python">                        <span class="n" style="color: #333;">add_sizes</span><span class="p">,</span> <span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">make_fs_access</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">)))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC855" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC856" class="line" lang="python">                <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">loc_to_path</span><span class="p">(</span><span class="n" style="color: #333;">obj</span><span class="p">):</span>  <span class="c1" style="color: #998; font-style: italic;"># type: (Dict[Text, Any]) -> None</span></span>

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<td class="diff-line-num old_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC857" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">field</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"path"</span><span class="p">,</span> <span class="s" style="color: #d14;">"nameext"</span><span class="p">,</span> <span class="s" style="color: #d14;">"nameroot"</span><span class="p">,</span> <span class="s" style="color: #d14;">"dirname"</span><span class="p">):</span></span>

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<br>

</li>

<li id="16fce72f6e9f404418a9d668d41e4181bb3abe61">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#16fce72f6e9f404418a9d668d41e4181bb3abe61"><strong>cwltool/provenance.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -305,9 +305,11 @@ class ProvenanceProfile():</td>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python">                 <span class="n" style="color: #333;">host_provenance</span><span class="p">,</span>        <span class="c1" style="color: #998; font-style: italic;"># type: bool</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python">                 <span class="n" style="color: #333;">user_provenance</span><span class="p">,</span>        <span class="c1" style="color: #998; font-style: italic;"># type: bool</span></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python">                 <span class="n" style="color: #333;">orcid</span><span class="p">,</span>                  <span class="c1" style="color: #998; font-style: italic;"># type: str</span></span>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python">                 <span class="n" style="color: #333;">fsaccess</span><span class="p">,</span>               <span class="c1" style="color: #998; font-style: italic;"># type: StdFsAccess</span></span>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python">                 <span class="n" style="color: #333;">run_uuid</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span>           <span class="c1" style="color: #998; font-style: italic;"># type: Optional[uuid.UUID]</span></span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python">                <span class="p">):</span>  <span class="c1" style="color: #998; font-style: italic;"># type: (...) -> None</span></span>

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<td class="diff-line-num old_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python">        <span class="s" style="color: #d14;">"""Initialize the provenance profile."""</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fsaccess</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fsaccess</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orcid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orcid</span></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_object</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">research_object</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_object</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -504,8 +506,7 @@ class ProvenanceProfile():</td>

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">entity</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'location'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">value</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC507" class="line" lang="python">            <span class="n" style="color: #333;">location</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">[</span><span class="s" style="color: #d14;">'location'</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># If we made it here, we'll have to add it to the RO</span></span>

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<pre style="margin: 0;">-<span id="LC507" class="line" lang="python">            <span class="n" style="color: #333;">fsaccess</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StdFsAccess</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC508" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">fsaccess</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">location</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fhandle</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fsaccess</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">location</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fhandle</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python">                <span class="n" style="color: #333;">relative_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_object</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_data_file</span><span class="p">(</span><span class="n" style="color: #333;">fhandle</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC511" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># FIXME: This naively relies on add_data_file setting hash as filename</span></span>

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python">                <span class="n" style="color: #333;">checksum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PurePath</span><span class="p">(</span><span class="n" style="color: #333;">relative_path</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -545,7 +546,12 @@ class ProvenanceProfile():</td>

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Check for secondaries</span></span>

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<pre style="margin: 0;"> <span id="LC547" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"secondaryFiles"</span><span class="p">,</span> <span class="p">()):</span></span>

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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># TODO: Record these in a specializationOf entity with UUID?</span></span>

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<pre style="margin: 0;">-<span id="LC548" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sec_entity</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">declare_file</span><span class="p">(</span><span class="n" style="color: #333;">sec</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sec</span><span class="p">[</span><span class="s" style="color: #d14;">'class'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"File"</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC550" class="line" lang="python">                <span class="p">(</span><span class="n" style="color: #333;">sec_entity</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">declare_file</span><span class="p">(</span><span class="n" style="color: #333;">sec</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">sec</span><span class="p">[</span><span class="s" style="color: #d14;">'class'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Directory"</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC552" class="line" lang="python">                <span class="n" style="color: #333;">sec_entity</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">declare_directory</span><span class="p">(</span><span class="n" style="color: #333;">sec</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Got unexpected secondaryFiles value: {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sec</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC555" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># We don't know how/when/where the secondary file was generated,</span></span>

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># but CWL convention is a kind of summary/index derived</span></span>

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># from the original file. As its generally in a different format</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -592,8 +598,7 @@ class ProvenanceProfile():</td>

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<pre style="margin: 0;"> <span id="LC598" class="line" lang="python">        <span class="n" style="color: #333;">is_empty</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;"> <span id="LC599" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC600" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"listing"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">value</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC595" class="line" lang="python">            <span class="n" style="color: #333;">fsaccess</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StdFsAccess</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC596" class="line" lang="python">            <span class="n" style="color: #333;">get_listing</span><span class="p">(</span><span class="n" style="color: #333;">fsaccess</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python">            <span class="n" style="color: #333;">get_listing</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fsaccess</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC602" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">entry</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"listing"</span><span class="p">,</span> <span class="p">[]):</span></span>

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<pre style="margin: 0;"> <span id="LC603" class="line" lang="python">            <span class="n" style="color: #333;">is_empty</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC604" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Declare child-artifacts</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -796,10 +801,13 @@ class ProvenanceProfile():</td>

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<pre style="margin: 0;"> <span id="LC801" class="line" lang="python">                <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">name</span></span>

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<pre style="margin: 0;"> <span id="LC802" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">job_order</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

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<pre style="margin: 0;"> <span id="LC803" class="line" lang="python">                <span class="n" style="color: #333;">prov_role</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wf_ns</span><span class="p">[</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">)]</span></span>

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<pre style="margin: 0;">-<span id="LC799" class="line" lang="python">                <span class="n" style="color: #333;">entity</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">declare_artefact</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC800" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">document</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">used</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC801" class="line" lang="python">                    <span class="n" style="color: #333;">process_run_id</span><span class="p">,</span> <span class="n" style="color: #333;">entity</span><span class="p">,</span> <span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">now</span><span class="p">(),</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC802" class="line" lang="python">                    <span class="p">{</span><span class="s" style="color: #d14;">"prov:role"</span><span class="p">:</span> <span class="n" style="color: #333;">prov_role</span><span class="p">})</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

804

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<pre style="margin: 0;">+<span id="LC804" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="diff-line-num new new_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC805" class="line" lang="python">                    <span class="n" style="color: #333;">entity</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">declare_artefact</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC806" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">document</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">used</span><span class="p">(</span></span>

</pre>

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807

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<pre style="margin: 0;">+<span id="LC807" class="line" lang="python">                        <span class="n" style="color: #333;">process_run_id</span><span class="p">,</span> <span class="n" style="color: #333;">entity</span><span class="p">,</span> <span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">now</span><span class="p">(),</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC808" class="line" lang="python">                        <span class="p">{</span><span class="s" style="color: #d14;">"prov:role"</span><span class="p">:</span> <span class="n" style="color: #333;">prov_role</span><span class="p">})</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC809" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC810" class="line" lang="python">                    <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC811" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC812" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_output_prov</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

805

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<td class="diff-line-num new_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

813

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<pre style="margin: 0;"> <span id="LC813" class="line" lang="python">                             <span class="n" style="color: #333;">final_output</span><span class="p">,</span>    <span class="c1" style="color: #998; font-style: italic;"># type: Union[Dict[Text, Any], List[Dict[Text, Any]]]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -937,8 +945,8 @@ class ProvenanceProfile():</td>

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<td class="diff-line-num old_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

937

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<td class="diff-line-num new_line" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

945

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<pre style="margin: 0;"> <span id="LC945" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ResearchObject</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

938

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<td class="diff-line-num new_line" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

946

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<pre style="margin: 0;"> <span id="LC946" class="line" lang="python">    <span class="s" style="color: #d14;">"""CWLProv Research Object."""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

939

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<td class="diff-line-num new_line" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

947

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<pre style="margin: 0;"> <span id="LC947" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

940

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<td class="diff-line-num new_line old" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC940" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">temp_prefix_ro</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"tmp"</span><span class="p">,</span> <span class="n" style="color: #333;">orcid</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">full_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

941

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<td class="diff-line-num new_line old" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC941" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># type: (str, Text, Text) -> None</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

948

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<pre style="margin: 0;">+<span id="LC948" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">fsaccess</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">temp_prefix_ro</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"tmp"</span><span class="p">,</span> <span class="n" style="color: #333;">orcid</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">full_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

949

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC949" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># type: (<span class="idiff left right">StdFsAccess, </span>str, Text, Text) -> None</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

942

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<td class="diff-line-num new_line" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

950

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<pre style="margin: 0;"> <span id="LC950" class="line" lang="python">        <span class="s" style="color: #d14;">"""Initialize the ResearchObject."""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

943

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<td class="diff-line-num new_line" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

951

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<pre style="margin: 0;"> <span id="LC951" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">temp_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp_prefix_ro</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

944

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<td class="diff-line-num new_line" data-linenumber="952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

952

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<pre style="margin: 0;"> <span id="LC952" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orcid</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">orcid</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">_valid_orcid</span><span class="p">(</span><span class="n" style="color: #333;">orcid</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -954,7 +962,7 @@ class ResearchObject():</td>

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<td class="diff-line-num old_line" data-linenumber="954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

954

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<td class="diff-line-num new_line" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

962

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<pre style="margin: 0;"> <span id="LC962" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_external_aggregates</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span>  <span class="c1" style="color: #998; font-style: italic;"># type: List[Dict[Text, Text]]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

955

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<td class="diff-line-num new_line" data-linenumber="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

963

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC963" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotations</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span>  <span class="c1" style="color: #998; font-style: italic;"># type: List[Dict[Text, Any]]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

956

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<td class="diff-line-num new_line" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

964

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<pre style="margin: 0;"> <span id="LC964" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_content_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span>  <span class="c1" style="color: #998; font-style: italic;"># type: Dict[Text,str]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

957

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<td class="diff-line-num new_line old" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC957" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

965

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<pre style="margin: 0;">+<span id="LC965" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fsaccess</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fsaccess</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

958

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<td class="diff-line-num new_line" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

966

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<pre style="margin: 0;"> <span id="LC966" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># These should be replaced by generate_prov_doc when workflow/run IDs are known:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

959

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<td class="diff-line-num new_line" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

967

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<pre style="margin: 0;"> <span id="LC967" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">engine_uuid</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"urn:uuid:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">uuid</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uuid4</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

960

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<td class="diff-line-num new_line" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

968

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<pre style="margin: 0;"> <span id="LC968" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ro_uuid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uuid</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uuid4</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1553,8 +1561,7 @@ class ResearchObject():</td>

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<td class="diff-line-num old_line" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1553

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<td class="diff-line-num new_line" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1561

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<pre style="margin: 0;"> <span id="LC1561" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Register in RO; but why was this not picked</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1554

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<td class="diff-line-num new_line" data-linenumber="1562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1562

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<pre style="margin: 0;"> <span id="LC1562" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># up by used_artefacts?</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1555

</td>

<td class="diff-line-num new_line" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1563

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<pre style="margin: 0;"> <span id="LC1563" class="line" lang="python">                    <span class="n" style="color: #333;">_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"[provenance] Adding to RO </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span><span class="p">,</span> <span class="n" style="color: #333;">structure</span><span class="p">[</span><span class="s" style="color: #d14;">"location"</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1556

</td>

<td class="diff-line-num new_line old" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1556" class="line" lang="python">                    <span class="n" style="color: #333;">fsaccess</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StdFsAccess</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1557

</td>

<td class="diff-line-num new_line old" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1557" class="line" lang="python">                    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">fsaccess</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">structure</span><span class="p">[</span><span class="s" style="color: #d14;">"location"</span><span class="p">],</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fp</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1564

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<pre style="margin: 0;">+<span id="LC1564" class="line" lang="python">                    <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fsaccess</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">structure</span><span class="p">[</span><span class="s" style="color: #d14;">"location"</span><span class="p">],</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fp</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1558

</td>

<td class="diff-line-num new_line" data-linenumber="1565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1565

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<pre style="margin: 0;"> <span id="LC1565" class="line" lang="python">                        <span class="n" style="color: #333;">relative_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_data_file</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1559

</td>

<td class="diff-line-num new_line" data-linenumber="1566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1566

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<pre style="margin: 0;"> <span id="LC1566" class="line" lang="python">                        <span class="n" style="color: #333;">checksum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PurePosixPath</span><span class="p">(</span><span class="n" style="color: #333;">relative_path</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1560

</td>

<td class="diff-line-num new_line" data-linenumber="1567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1567

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<pre style="margin: 0;"> <span id="LC1567" class="line" lang="python">                        <span class="n" style="color: #333;">structure</span><span class="p">[</span><span class="s" style="color: #d14;">"checksum"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s$</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">SHA1</span><span class="p">,</span> <span class="n" style="color: #333;">checksum</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1572,7 +1579,10 @@ class ResearchObject():</td>

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<td class="diff-line-num old_line" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1572

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<td class="diff-line-num new_line" data-linenumber="1579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1579

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<pre style="margin: 0;"> <span id="LC1579" class="line" lang="python">                <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">structure</span><span class="p">[</span><span class="s" style="color: #d14;">"location"</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1573

</td>

<td class="diff-line-num new_line" data-linenumber="1580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1580

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1580" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1574

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<td class="diff-line-num new_line" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1581

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<pre style="margin: 0;"> <span id="LC1581" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">val</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">structure</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1575

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<td class="diff-line-num new_line old" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1575" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_relativise_files</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1582

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<pre style="margin: 0;">+<span id="LC1582" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1583

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<pre style="margin: 0;">+<span id="LC1583" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_relativise_files</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1584" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1585

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<pre style="margin: 0;">+<span id="LC1585" class="line" lang="python">                    <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1576

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<td class="diff-line-num new_line" data-linenumber="1586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1586

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<pre style="margin: 0;"> <span id="LC1586" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1587

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<pre style="margin: 0;"> <span id="LC1587" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1588" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">structure</span><span class="p">,</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">Text</span><span class="p">)):</span></span>

</pre>

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<br>

</li>

<li id="e4186687ed9ace3055434ea5fdd184601e544d69">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#e4186687ed9ace3055434ea5fdd184601e544d69"><strong>cwltool/singularity.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,6 +118,8 @@ class SingularityCommandLineJob(ContainerCommandLineJob):</td>

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<td class="diff-line-num new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">match</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python">                <span class="n" style="color: #333;">dockerRequirement</span><span class="p">[</span><span class="s" style="color: #d14;">"dockerPull"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"docker://"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dockerRequirement</span><span class="p">[</span><span class="s" style="color: #d14;">"dockerPull"</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">"dockerImageId"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dockerRequirement</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">dockerRequirement</span><span class="p">[</span><span class="s" style="color: #d14;">'dockerImageId'</span><span class="p">]):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python">                <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">            <span class="n" style="color: #333;">candidates</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">dockerRequirement</span><span class="p">[</span><span class="s" style="color: #d14;">'dockerImageId'</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python">            <span class="n" style="color: #333;">candidates</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">_normalize_image_id</span><span class="p">(</span><span class="n" style="color: #333;">dockerRequirement</span><span class="p">[</span><span class="s" style="color: #d14;">'dockerImageId'</span><span class="p">]))</span></span>

</pre>

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125

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_version_3_or_newer</span><span class="p">():</span></span>

</pre>

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<br>

</li>

<li id="981a72379b95d1fc9d93c9d8380918dd3ab82e9e">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#981a72379b95d1fc9d93c9d8380918dd3ab82e9e"><strong>cwltool/workflow.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -522,7 +522,8 @@ class Workflow(Process):</td>

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<pre style="margin: 0;"> <span id="LC522" class="line" lang="python">                <span class="n" style="color: #333;">host_provenance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loadingContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">host_provenance</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

523

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<td class="diff-line-num new_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC523" class="line" lang="python">                <span class="n" style="color: #333;">user_provenance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loadingContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">user_provenance</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

524

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<td class="diff-line-num new_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

524

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<pre style="margin: 0;"> <span id="LC524" class="line" lang="python">                <span class="n" style="color: #333;">orcid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loadingContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orcid</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

525

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<td class="diff-line-num new_line old" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python">                <span class="n" style="color: #333;">run_uuid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">run_uuid</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># inherit RO UUID for master wf run</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC525" class="line" lang="python">                <span class="n" style="color: #333;">run_uuid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">run_uuid</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python">                <span class="n" style="color: #333;">fsaccess</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loadingContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fsaccess</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># inherit RO UUID for master wf run</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

526

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<td class="diff-line-num new_line" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

527

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<pre style="margin: 0;"> <span id="LC527" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># TODO: Is Workflow(..) only called when we are the master workflow?</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

527

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<td class="diff-line-num new_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

528

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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent_wf</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">provenance_object</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

528

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<td class="diff-line-num new_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

529

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<pre style="margin: 0;"> <span id="LC529" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -582,6 +583,7 @@ class Workflow(Process):</td>

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<td class="diff-line-num old_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

582

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<td class="diff-line-num new_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

583

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<pre style="margin: 0;"> <span id="LC583" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_obj</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

583

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<td class="diff-line-num new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

584

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<pre style="margin: 0;"> <span id="LC584" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toplevel</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

584

</td>

<td class="diff-line-num new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

585

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<pre style="margin: 0;"> <span id="LC585" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Record primary-job.json</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

586

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<pre style="margin: 0;">+<span id="LC586" class="line" lang="python">                <span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fsaccess</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">make_fs_access</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

585

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<td class="diff-line-num new_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

587

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<pre style="margin: 0;"> <span id="LC587" class="line" lang="python">                <span class="n" style="color: #333;">runtimeContext</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">research_obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_job</span><span class="p">(</span><span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">job</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">job</span><span class="p">)</span></span>

</pre>

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586

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<td class="diff-line-num new_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC588" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC589" class="line" lang="python">        <span class="n" style="color: #333;">job</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WorkflowJob</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">runtimeContext</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">cwltool (1.0.20190915164430+dfsg-1) unstable; urgency=medium</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 15 Sep 2019 21:17:19 +0200</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">cwltool (1.0.20190815141648+dfsg-2) unstable; urgency=medium</span>

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  * Fix AutoPkgTest requirements (Closes: #935579)</span>

</pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,6 +5,7 @@ Section: science</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">               dh-python,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">               procps,</span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">               python3,</span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">               python3-all,</span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">               python3-setuptools,</span>

</pre>

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<br>

</li>

<li id="fcb92b9accd9db58b837ef9c16090c7d4830a9f9">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#fcb92b9accd9db58b837ef9c16090c7d4830a9f9"><strong>debian/patches/disable_prov</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,10 +75,11 @@ Description: Disable --provance until python3-proc issue is resolved</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> # Module to be tested</span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> from cwltool import load_tool, provenance</span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> from cwltool.main import main</span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="p">@@ -48,635 +46,4 @@</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="p">@@ -48,636 +46,3 @@</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff">     if not os.environ.get("DEBUG"):</span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff">         shutil.rmtree(directory)</span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span></span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-def cwltool(folder, *args):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    new_args = ['--provenance', folder]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -544,7 +545,7 @@ Description: Disable --provance until python3-proc issue is resolved</td>

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-@pytest.fixture</span></span>

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<pre style="margin: 0;"> <span id="LC547" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-def research_object():</span></span>

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<td class="diff-line-num new_line old" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC547" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    re_ob = provenance.ResearchObject()</span></span>

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<td class="diff-line-num new old_line" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    re_ob = provenance.ResearchObject(<span class="idiff left right">StdFsAccess('')</span>)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC549" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    yield re_ob</span></span>

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<td class="diff-line-num new_line" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC550" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    re_ob.close()</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC551" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -711,4 +712,3 @@ Description: Disable --provance until python3-proc issue is resolved</td>

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Reasearch object may need to be pickled (for Toil)</span></span>

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<pre style="margin: 0;"> <span id="LC713" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-def test_research_object_picklability(research_object):</span></span>

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<pre style="margin: 0;"> <span id="LC714" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    assert pickle.dumps(research_object) is not None</span></span></pre>

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<pre style="margin: 0;">-<span id="LC714" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# For now, we do not ship the --provenance feature in Debian</span></span></pre>

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<br>

</li>

<li id="986d91bafce8bbac47e11e9d329955f76890bf0b">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#986d91bafce8bbac47e11e9d329955f76890bf0b"><strong>debian/patches/pytest</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +11,7 @@ Description: Deal with pytest 4.6 changes</td>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff">                     processes_to_kill, versionstring, visit_class,</span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff">                     windows_default_container_id)</span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> from .subgraph import get_subgraph</span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -41<span class="idiff left right">6,7 +416</span>,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -41<span class="idiff left right">7,7 +417</span>,7 @@</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff">         base = os.getcwd()</span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff">     visit_class(deps, ("File", "Directory"), functools.partial(</span>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff">         make_relative, base))</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,8 +20,8 @@ Description: Deal with pytest 4.6 changes</td>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> def prov_deps(obj,              # type: Mapping[Text, Any]</span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff">               document_loader,  # type: Loader</span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="p">@@ -49<span class="idiff left right">3,8 +493</span>,8 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff">          <span class="idiff left right">runtimeContext=None           # type: Optional[RuntimeContext]</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -49<span class="idiff left right">5,8 +495</span>,8 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff">          <span class="idiff left right">input_required=True           # type: bool</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff">         ):  # type: (...) -> int</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff">     if not stdout:  # force UTF-8 even if the console is configured differently</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        if (hasattr(sys.stdout, "encoding")</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@ Description: Deal with pytest 4.6 changes</td>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff">             if PY3 and hasattr(sys.stdout, "detach"):</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff">                 stdout = io.TextIOWrapper(sys.stdout.buffer, encoding='utf-8')</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff">             else:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="p">@@ -68<span class="idiff left right">1,7 +681</span>,7 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -68<span class="idiff left right">4,7 +684</span>,7 @@</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff">                     print_pack(loadingContext.loader, processobj, uri, metadata))</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff">             if args.print_pre:</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,7 +40,7 @@ Description: Deal with pytest 4.6 changes</td>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff">                 return 0</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff">             tool = make_tool(uri, loadingContext)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="p">@@ -7<span class="idiff left right">37,7 +737</span>,7 @@</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

43

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -7<span class="idiff left right">40,7 +740</span>,7 @@</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff">             if args.print_subgraph:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff">                 if "name" in tool.tool:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff">                     del tool.tool["name"]</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,7 +49,7 @@ Description: Deal with pytest 4.6 changes</td>

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49

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff">                 return 0</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> </span>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff">         except (validate.ValidationException) as exc:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="p">@@ -8<span class="idiff left right">49,7 +849</span>,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="p">@@ -8<span class="idiff left right">68,7 +868</span>,7 @@</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff">                 if isinstance(out, string_types):</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff">                     stdout.write(out)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff">                 else:</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,7 +71,7 @@ Description: Deal with pytest 4.6 changes</td>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cwltool.orig/tests/test_udocker.py</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cwltool/tests/test_udocker.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">7,12 +37</span>,9 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">8,12 +38</span>,9 @@</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff">                   break</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff">               subprocess.call(["rm", "./udocker"])</span>

</pre>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> </span>

</pre>

</td>

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</table>

<br>

</li>

<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-tests</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @, python3-pytest-xdist, python3-pytest-mock, python3-pytest-runner, nodejs, curl, python3-mock</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, python3-pytest-xdist, python3-pytest-mock, python3-pytest-runner, nodejs, curl, python3-mock<span class="idiff left right">, procps</span></span>

</pre>

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3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="aab2726ed6daf419caf178b1480b6d7da8a85af6">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#aab2726ed6daf419caf178b1480b6d7da8a85af6"><strong>debian/tests/run-tests</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,6 +6,7 @@ if [ "$ADTTMP" = "" ] ; then</td>

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6

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ADTTMP</span><span class="s2" style="color: #d14;">"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ADTTMP</span><span class="k" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nv" style="color: #008080;">SKIPS</span><span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># if [ "$(id -u)" -eq 0 ]; then</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f"><strong>setup.cfg</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,6 +13,6 @@ addopts = --ignore cwltool/schemas --basetemp ./tmp</td>

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13

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">testpaths = tests</span>

</pre>

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14

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14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">[egg_info]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="diff-line-num new_line old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">tag_build = .20190<span class="idiff left right">815141648</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">tag_build = .20190<span class="idiff left right">915164430</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">tag_date = 0</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span></pre>

</td>

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</table>

<br>

</li>

<li id="48a232f5e05cbaa234aa30dfa88a8d19bc10a1bc">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#48a232f5e05cbaa234aa30dfa88a8d19bc10a1bc"><strong>tests/arg-empty-prefix-separate-false.cwl</strong></a>

<hr>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">class: CommandLineTool</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">cwlVersion: v1.0</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">baseCommand: []</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">inputs:</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  echo: boolean</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">outputs: []</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">arguments:</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">- position: 1</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  shellQuote: false</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">  prefix: ''</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">  valueFrom: "non_existing_app"</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">- position: 0</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">  prefix: ''</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">  separate: false</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">  shellQuote: false</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">  valueFrom: "echo"</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">requirements:</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">- class: ShellCommandRequirement</span></pre>

</td>

</tr>

<tr class="line_holder new-nonewline" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa"></td>

<td class="new_line diff-line-num" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa"></td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>

</tr>

</table>

<br>

</li>

<li id="6114135dd99d21b62b938d64cf9260a92d1f1416">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#6114135dd99d21b62b938d64cf9260a92d1f1416"><strong>tests/env.cwl</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/env cwl-runner</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">cwlVersion: v1.0</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">class: CommandLineTool</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">inputs: []</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="98c1e4d87524a5347c05bae01246f5c25bd6bd48">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#98c1e4d87524a5347c05bae01246f5c25bd6bd48"><strong>tests/env2.cwl</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/env cwl-runner</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">cwlVersion: v1.0</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">class: CommandLineTool</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">inputs: []</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">requirements:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  ShellCommandRequirement: {}</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">baseCommand: echo</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">arguments:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  - valueFrom: ></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">      {\\"env_listing\\": \\"\$(env)\\"}</span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">    shellQuote: False</span>

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">stdout: cwl.output.json</span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">outputs:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">  env_listing: string</span></pre>

</td>

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</table>

<br>

</li>

<li id="a4d3b8d2921c82c34c5afa41066477aba090b135">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#a4d3b8d2921c82c34c5afa41066477aba090b135"><strong>tests/secondary-files-string-v1.cwl</strong></a>

<hr>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/env cwl-runner</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">cwlVersion: v1.0</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">class: CommandLineTool</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">baseCommand:</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,4 +17,4 @@ outputs:</td>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">    type: File</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">    secondaryFiles: ^.fastq</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">    outputBinding:</span>

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">      glob: $(inputs.fasta_path.basename)</span></pre>

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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">      glob: $(inputs.fasta_path.basename)</span></pre>

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<br>

</li>

<li id="c850a901a4677d28f381ddf53272d079cf0d4ae0">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#c850a901a4677d28f381ddf53272d079cf0d4ae0"><strong>tests/test_examples.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,7 @@ from cwltool.utils import onWindows</td>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cwltool.resolver</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cwltool.process</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">CWL_IANA</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cwltool.sandboxjs</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">JavascriptException</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">get_data</span><span class="p">,</span> <span class="n" style="color: #333;">get_main_output</span><span class="p">,</span> <span class="n" style="color: #333;">get_windows_safe_factory</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">get_data</span><span class="p">,</span> <span class="n" style="color: #333;">get_main_output</span><span class="p">,</span> <span class="n" style="color: #333;">get_windows_safe_factory</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">subprocess</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python">                   <span class="n" style="color: #333;">needs_docker</span><span class="p">,</span> <span class="n" style="color: #333;">working_directory</span><span class="p">,</span> <span class="n" style="color: #333;">needs_singularity</span><span class="p">,</span> <span class="n" style="color: #333;">temp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">windows_needs_docker</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">six</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -954,7 +954,7 @@ def test_bad_userspace_runtime(factor):</td>

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<pre style="margin: 0;"> <span id="LC954" class="line" lang="python">        <span class="s" style="color: #d14;">"--user-space-docker-cmd=quaquioN"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--default-container=debian"</span><span class="p">,</span></span>

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<td class="diff-line-num new_line" data-linenumber="955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC955" class="line" lang="python">        <span class="n" style="color: #333;">get_data</span><span class="p">(</span><span class="n" style="color: #333;">test_file</span><span class="p">),</span> <span class="n" style="color: #333;">get_data</span><span class="p">(</span><span class="n" style="color: #333;">job_file</span><span class="p">)])</span></span>

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<td class="diff-line-num new_line" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC956" class="line" lang="python">    <span class="n" style="color: #333;">error_code</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_main_output</span><span class="p">(</span><span class="n" style="color: #333;">commands</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC957" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"<span class="idiff left right">'quaquioN' not found:</span>"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span></span>

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<pre style="margin: 0;">+<span id="LC957" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"<span class="idiff left right">or quaquioN is missing or broken</span>"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span></span>

</pre>

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958

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<td class="diff-line-num new_line" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

958

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<pre style="margin: 0;"> <span id="LC958" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">error_code</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

959

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<td class="diff-line-num new_line" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

959

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<pre style="margin: 0;"> <span id="LC959" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

960

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<td class="diff-line-num new_line" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

960

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<pre style="margin: 0;"> <span id="LC960" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">windows_needs_docker</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1011,10 +1011,38 @@ def test_env_filtering(factor):</td>

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1011

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<td class="diff-line-num new_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1011

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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="python">    <span class="n" style="color: #333;">commands</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="n" style="color: #333;">get_data</span><span class="p">(</span><span class="n" style="color: #333;">test_file</span><span class="p">)])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1012

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<td class="diff-line-num new_line" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1012

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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="python">    <span class="n" style="color: #333;">error_code</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_main_output</span><span class="p">(</span><span class="n" style="color: #333;">commands</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1013

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<td class="diff-line-num new_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1013

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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1014

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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="python">    <span class="n" style="color: #333;">process</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span><span class="s" style="color: #d14;">"sh"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-c"</span><span class="p">,</span> <span class="s" style="color: #d14;">r"""getTrueShellExeName() {</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1015

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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="python"><span class="s" style="color: #d14;">  local trueExe nextTarget 2>/dev/null</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1016

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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="python"><span class="s" style="color: #d14;">  trueExe=$(ps -o comm= $$) || return 1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1017

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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="python"><span class="s" style="color: #d14;">  [ "${trueExe#-}" = "$trueExe" ] || trueExe=${trueExe#-}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1018

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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="python"><span class="s" style="color: #d14;">  [ "${trueExe#/}" != "$trueExe" ] || trueExe=$([ -n "$ZSH_VERSION" ] && which -p "$trueExe" || which "$trueExe")</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1019

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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="python"><span class="s" style="color: #d14;">  while nextTarget=$(readlink "$trueExe"); do trueExe=$nextTarget; done</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1020

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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="python"><span class="s" style="color: #d14;">  printf '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s\n' "$(basename "$trueExe")"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1021

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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="python"><span class="s" style="color: #d14;">} ; getTrueShellExeName"""</span><span class="p">],</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span> <span class="n" style="color: #333;">env</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1022

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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="python">    <span class="n" style="color: #333;">sh_name</span><span class="p">,</span> <span class="n" style="color: #333;">sh_name_err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1023

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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="python">    <span class="n" style="color: #333;">sh_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sh_name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>

</pre>

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</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1024

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1024" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1014

</td>

<td class="diff-line-num new_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1025

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1025" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"completed success"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">error_code</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1015

</td>

<td class="diff-line-num new_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1026

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1026" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">error_code</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">error_code</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1016

</td>

<td class="diff-line-num new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1027

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1027" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">onWindows</span><span class="p">():</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1017

</td>

<td class="diff-line-num new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1028

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1028" class="line" lang="python">        <span class="n" style="color: #333;">target</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1018

</td>

<td class="diff-line-num new_line old" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1018" class="line" lang="python">    <span class="k" style="font-weight: 600;">el<span class="idiff left right">se</span></span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1029

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1029" class="line" lang="python">    <span class="k" style="font-weight: 600;">el<span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sh_name</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"dash"</span></span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1019

</td>

<td class="diff-line-num new_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1030

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1030" class="line" lang="python">        <span class="n" style="color: #333;">target</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1020

</td>

<td class="diff-line-num new_line old" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1020" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">)[</span><span class="s" style="color: #d14;">'env_count'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">error_code</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="p">)</span></span></pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1031

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1031" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># bash adds "SHLVL" and "_" environment variables</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1032

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1032" class="line" lang="python">        <span class="n" style="color: #333;">target</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1033

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1033" class="line" lang="python">    <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">)[</span><span class="s" style="color: #d14;">'env_count'</span><span class="p">]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1034

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1034" class="line" lang="python">    <span class="n" style="color: #333;">details</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1035

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1035" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">target</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1036

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1036" class="line" lang="python">        <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">details</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_main_output</span><span class="p">([</span><span class="s" style="color: #d14;">"--quiet"</span><span class="p">,</span> <span class="n" style="color: #333;">get_data</span><span class="p">(</span><span class="s" style="color: #d14;">"tests/env2.cwl"</span><span class="p">)])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1037

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1037" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">sh_name</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1038

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1038" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">sh_name_err</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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</td>

<td class="diff-line-num new new_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1039

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1039" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">details</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1040

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1040" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">error_code</span><span class="p">,</span> <span class="n" style="color: #333;">sh_name</span><span class="p">,</span> <span class="n" style="color: #333;">sh_name_err</span><span class="p">,</span> <span class="n" style="color: #333;">details</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1041

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1041" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1042

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1042" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">windows_needs_docker</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1043

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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_v1_0_arg_empty_prefix_separate_false</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1044

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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="python">    <span class="n" style="color: #333;">test_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"tests/arg-empty-prefix-separate-false.cwl"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1045

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1045" class="line" lang="python">    <span class="n" style="color: #333;">error_code</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_main_output</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1046

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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="python">        <span class="p">[</span><span class="s" style="color: #d14;">'--debug'</span><span class="p">,</span> <span class="n" style="color: #333;">get_data</span><span class="p">(</span><span class="n" style="color: #333;">test_file</span><span class="p">),</span> <span class="s" style="color: #d14;">"--echo"</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1047

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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"completed success"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">stderr</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1048

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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">error_code</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span></pre>

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<br>

</li>

<li id="7593f63b8b7959e775e8a25fcf434451b4da06a7">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#7593f63b8b7959e775e8a25fcf434451b4da06a7"><strong>tests/test_provenance.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,6 +24,7 @@ from cwltool import load_tool, provenance</td>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cwltool.main</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">main</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cwltool.resolver</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cwltool.context</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">RuntimeContext</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cwltool.stdfsaccess</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StdFsAccess</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_data</span><span class="p">,</span> <span class="n" style="color: #333;">needs_docker</span><span class="p">,</span> <span class="n" style="color: #333;">temp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">working_directory</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -513,7 +514,7 @@ def check_prov(base_path, nested=False, single_tool=False, directory=False,</td>

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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC515" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fixture</span></span>

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<pre style="margin: 0;"> <span id="LC516" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">research_object</span><span class="p">():</span></span>

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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python">    <span class="n" style="color: #333;">re_ob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">provenance</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ResearchObject</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python">    <span class="n" style="color: #333;">re_ob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">provenance</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ResearchObject</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">StdFsAccess</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">''</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

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<td class="diff-line-num new_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python">    <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">re_ob</span></span>

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<td class="diff-line-num new_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python">    <span class="n" style="color: #333;">re_ob</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python"></span>

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<br>

</li>

<li id="6a7cf45dc67d70001b23638ee84abceec3fe8f84">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#6a7cf45dc67d70001b23638ee84abceec3fe8f84"><strong>tests/test_toolargparse.py</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">tempfile</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NamedTemporaryFile</span></span>

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">io</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BytesIO</span><span class="p">,</span> <span class="n" style="color: #333;">StringIO</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cwltool.main</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">main</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">cwltool.executors</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_data</span><span class="p">,</span> <span class="n" style="color: #333;">needs_docker</span></span>

</pre>

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8

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">script_a</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'''</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">#!/usr/bin/env cwl-runner</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">cwlVersion: v1.0</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -94,3 +96,43 @@ def test_argparse(name, script_contents, params, tmpdir):</td>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python">    <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">script</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python">            <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NoopJobExecutor</span><span class="p">(</span><span class="n" style="color: #333;">cwltool</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">executors</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">JobExecutor</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_jobs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python">                 <span class="n" style="color: #333;">process</span><span class="p">,</span>           <span class="c1" style="color: #998; font-style: italic;"># type: Process</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python">                 <span class="n" style="color: #333;">job_order_object</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;"># type: Dict[Text, Any]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python">                 <span class="n" style="color: #333;">logger</span><span class="p">,</span>            <span class="c1" style="color: #998; font-style: italic;"># type: logging.Logger</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python">                 <span class="n" style="color: #333;">runtime_context</span>     <span class="c1" style="color: #998; font-style: italic;"># type: RuntimeContext</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python">                <span class="p">):</span>  <span class="c1" style="color: #998; font-style: italic;"># type: (...) -> None</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

110

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">execute</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python">                <span class="n" style="color: #333;">process</span><span class="p">,</span>           <span class="c1" style="color: #998; font-style: italic;"># type: Process</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python">                <span class="n" style="color: #333;">job_order_object</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;"># type: Dict[Text, Any]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python">                <span class="n" style="color: #333;">runtime_context</span><span class="p">,</span>   <span class="c1" style="color: #998; font-style: italic;"># type: RuntimeContext</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python">                <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span>       <span class="c1" style="color: #998; font-style: italic;"># type: logging.Logger</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python">               <span class="p">):</span>  <span class="c1" style="color: #998; font-style: italic;"># type: (...) -> Tuple[Optional[Union[Dict[Text, Any], List[Dict[Text, Any]]]], Text]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

116

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">{},</span> <span class="s" style="color: #d14;">"success"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_dont_require_inputs</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python">        <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BytesIO</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python">        <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python">    <span class="n" style="color: #333;">script</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

125

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC126" class="line" lang="python">        <span class="n" style="color: #333;">script</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w'</span><span class="p">,</span> <span class="n" style="color: #333;">delete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

127

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python">        <span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">script_a</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

128

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python">        <span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

129

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

130

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">argsl</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"--debug"</span><span class="p">,</span> <span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"--input"</span><span class="p">,</span> <span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">],</span> <span class="n" style="color: #333;">executor</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NoopJobExecutor</span><span class="p">(),</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stream</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

131

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">argsl</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"--debug"</span><span class="p">,</span> <span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">],</span> <span class="n" style="color: #333;">executor</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NoopJobExecutor</span><span class="p">(),</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stream</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

132

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">argsl</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"--debug"</span><span class="p">,</span> <span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">],</span> <span class="n" style="color: #333;">executor</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NoopJobExecutor</span><span class="p">(),</span> <span class="n" style="color: #333;">input_required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stream</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

133

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

134

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">SystemExit</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">err</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

135

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">code</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">name</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

136

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python">    <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

137

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">script</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

138

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python">            <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span></pre>

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<br>

</li>

<li id="172f21b418c7d70b9e17cff1ed0fc4d6036b4d7f">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#172f21b418c7d70b9e17cff1ed0fc4d6036b4d7f"><strong>tests/test_udocker.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,29 +10,30 @@ from psutil.tests import TRAVIS</td>

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10

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">LINUX</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">platform</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'linux'</span><span class="p">,</span> <span class="s" style="color: #d14;">'linux2'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">skipif</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">LINUX</span><span class="p">,</span> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"LINUX only"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#@pytest.mark.skipif(not LINUX, reason="LINUX only")</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">skip</span><span class="p">(</span><span class="s" style="color: #d14;">"Udocker install is broken, see https://github.com/indigo-dc/udocker/issues/221"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestUdocker</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python">    <span class="n" style="color: #333;">udocker_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setup_class</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python">        <span class="n" style="color: #333;">install_cmds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python">            <span class="s" style="color: #d14;">"curl https://raw.githubusercontent.com/indigo-dc/udocker/master/udocker.py -o ./udocker"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python">            <span class="s" style="color: #d14;">"chmod u+rx ./udocker"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python">            <span class="s" style="color: #d14;">"./udocker install"</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python">        <span class="n" style="color: #333;">test_cwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python">        <span class="n" style="color: #333;">test_environ</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python">        <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">docker_install_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdtemp</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">docker_install_dir</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">        <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"https://download.ncg.ingrid.pt/webdav/udocker/udocker-1.1.3.tar.gz"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">        <span class="n" style="color: #333;">install_cmds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">            <span class="p">[</span><span class="s" style="color: #d14;">"curl"</span><span class="p">,</span> <span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"./udocker-tarball.tgz"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">            <span class="p">[</span><span class="s" style="color: #d14;">"tar"</span><span class="p">,</span> <span class="s" style="color: #d14;">"xzvf"</span><span class="p">,</span> <span class="s" style="color: #d14;">"udocker-tarball.tgz"</span><span class="p">,</span> <span class="s" style="color: #d14;">"udocker"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">            <span class="p">[</span><span class="s" style="color: #d14;">"bash"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-c"</span><span class="p">,</span> <span class="s" style="color: #d14;">"UDOCKER_TARBALL={}/udocker-tarball.tgz ./udocker install"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">docker_install_dir</span><span class="p">)]]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">'UDOCKER_DIR'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">docker_install_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">".udocker"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">'HOME'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">docker_install_dir</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python">        <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC35" class="line" lang="python">              <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cmd</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">install_cmds</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="python">              <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="n" style="color: #333;">cmd<span class="idiff left">s</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cmds</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">install_cmds</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python">              <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python">                  <span class="k" style="font-weight: 600;">break</span></span>

</pre>

</td>

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38

</td>

<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python">              <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">([</span><span class="s" style="color: #d14;">"rm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"./udocker"</span><span class="p">])</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="4f5e5d8e9fca25e91732fa82113435fd58ffbc58">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#4f5e5d8e9fca25e91732fa82113435fd58ffbc58"><strong>tests/trs/md5sum-workflow.cwl</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/env cwl-runner</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">cwlVersion: v1.0</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">class: Workflow</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,4 +15,4 @@ steps:</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

</td>

<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">    run: md5sum-tool.cwl</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

</td>

<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">    in:</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

</td>

<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">      input_file: input_file</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

</td>

<td class="diff-line-num new_line old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">    out: [output_file]</span></pre>

</td>

</tr>

<tr class="line_holder old-nonewline" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa"></td>

<td class="new_line diff-line-num" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa"></td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">    out: [output_file]</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="e3a2c135872245be444d76de339dc087b299d383">

<a href="https://salsa.debian.org/med-team/cwltool/compare/920ab061279e860285ee4d97cb3c13de1c399340...b5a53e1c357c3f9071e67eb6ab6507e22ac2d141#e3a2c135872245be444d76de339dc087b299d383"><strong>tests/wf/optional-numerical-output-0.cwl</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/env cwl-runner</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">cwlVersion: v1.0</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">class: CommandLineTool</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">baseCommand:</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,4 +14,4 @@ outputs:</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

</td>

<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">    outputBinding:</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

</td>

<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">      glob: "a.txt"</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

</td>

<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">      loadContents: true</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">      outputEval: "${\n    return parseFloat(self[0].contents);\n}"</span></pre>

</td>

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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">      outputEval: "${\n    return parseFloat(self[0].contents);\n}"</span></pre>

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