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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/snakemake">Debian Med / snakemake</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/commit/2ae04d6a14bd6727c699236ef40493186a5731fb">2ae04d6a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-07-31T09:22:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.5.4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/commit/83fa8e5e36a9cd9799cf286e5564b1ddf4653692">83fa8e5e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-07-31T09:23:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.5.4'
Update to upstream version '5.5.4'
with Debian dir 56097cffc5945c72dfe93da70a2c54ed76a3d502</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/commit/776fde082b3d1a0b2d95761ccce17a6d8cc05335">776fde08</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-07-31T09:27:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">5.5.4-1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/commit/dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce">dbc52a27</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-07-31T14:26:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">run all of the tests
</pre>
</li>
</ul>
<h4>27 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#45267e3a9556cafa9cb7b61dab7a3b6659e73aad">
CHANGELOG.rst
</a>
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<li class="file-stats">
<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
debian/README.source
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<span class="new-file">
+
debian/docs
</span>
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<li class="file-stats">
<a href="#14311a7e2fde4d3f5412d248239270f0dcead73f">
debian/patches/0012-reproducible-build.patch
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<li class="file-stats">
<a href="#129f87da0c8d360881ba445e9228a00e19477a56">
<span class="new-file">
+
debian/patches/0013-remove-duplicate-keyword-argument.patch
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<li class="file-stats">
<a href="#3099d3b193ee5d195e9fef4d6fc3253cd1a1d175">
<span class="new-file">
+
debian/patches/boto3_is_just_boto
</span>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#85ccdeeb03055211183e48520592d9a93592b330">
debian/source/lintian-overrides
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<li class="file-stats">
<a href="#9617ea0d5d1a492cd381dd6bb688b8a5cbe6512b">
docs/getting_started/installation.rst
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<li class="file-stats">
<a href="#d0153cac95479af9bfb99b746b633bc8255bb53a">
docs/index.rst
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<li class="file-stats">
<a href="#a64f4e86841a3aed0cd5f5ec9d71431086ea0014">
docs/tutorial/advanced.rst
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<li class="file-stats">
<a href="#7f695df9a93bb6d2f47c562fd1282181e830528b">
docs/tutorial/basics.rst
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<li class="file-stats">
<a href="#54c391de2500e0856c23737daf64f9d931569110">
environment.yml
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<li class="file-stats">
<a href="#c2acba86d5ef7b186a3f54c5fcbfeeb889e18738">
misc/vim/syntax/snakemake.vim
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#5e16cbeea010f59dbef52f8950f4873c94f39c7e">
snakemake/_version.py
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<li class="file-stats">
<a href="#6c195c1be80e4ad60b55a5a06c27411c43bbc217">
snakemake/logging.py
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<li class="file-stats">
<a href="#3065d4749c6410564a20007bd7748abfda7699f6">
snakemake/report/__init__.py
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<li class="file-stats">
<a href="#7b2e7c5590f914b1c99d6d779757cc4e2527cd59">
snakemake/report/report.html
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<li class="file-stats">
<a href="#55752111e76e9d786fdb84c4e7fd9f6de5c67a24">
snakemake/rules.py
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<li class="file-stats">
<a href="#66a73d9dd46eb8e71f0039a18d36dbd78aea7977">
snakemake/script.py
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<li class="file-stats">
<a href="#cb9e107597e441fb1c0d61663359d9cf1dbfe04d">
snakemake/workflow.py
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<li class="file-stats">
<a href="#d1deee71de70305809d43086b13f7eb407aff6f2">
test-environment.yml
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<li class="file-stats">
<a href="#49b1347c0e01c75480e0e6643f830d8312c26576">
tests/test_report/expected-results/report.html
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</ul>
<h4>Changes:</h4>
<li id="45267e3a9556cafa9cb7b61dab7a3b6659e73aad">
<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#45267e3a9556cafa9cb7b61dab7a3b6659e73aad"><strong>CHANGELOG.rst</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[5.5.4] - 2019-07-21</span>
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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">
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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="LC2" class="line" lang="plaintext">====================</span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Changed</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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<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">-------</span>
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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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">- Reports now automatically include workflow code and configuration for improved transparency.</span>
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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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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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">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">[5.5.3] - 2019-07-11</span>
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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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">====================</span>
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Changed</span>
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<br>
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<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
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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">@@ -13,3 +13,17 @@ with in 0011-fix-privacy-breach.patch. Here are the remaining issues:</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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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> should be packaged to solve the two remaining issues.</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 12 Dec 2017 11:32:28 +0100</span>
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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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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Missing (optional) dependencies:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">- conda</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">- gfal-copy and other gfal-* commands for gfal/gridftp (missing from gfal2?)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Missing (optional) Python dependencies:</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">- moto</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">- google.cloud (google-cloud-sdk)</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">- ftputil</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">- pysftp</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">- XRootD</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">- aioeasywebdav</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">snakemake (5.5.<span class="idiff left right">3-2</span>) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">snakemake (5.5.<span class="idiff left right">4-1</span>) UNRELEASED; urgency=medium</span>
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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"> [ Dylan Aïssi ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Apply patch from Chris Lamb to make the build reproducible</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> (Closes: #932116).</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org> Tue, 16 Jul 2019 08:13:48 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * New upstream release</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * debian/control: Add missing build-deps (as shown in errors during the</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> documenation building)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * debian/README.source: Document missing (optional?) dependencies</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * debian/rules: Fix test invocation, as almost all tests were missed;</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> Document what is known about the skipped tests</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Apply patch from upstream to fix duplicated argument (Closes: #933527)</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Wed, 31 Jul 2019 11:24:24 +0200</span>
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7
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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8
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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">snakemake (5.5.3-1) unstable; urgency=medium</span>
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9
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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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">@@ -6,10 +6,15 @@ Priority: optional</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> ca-certificates,</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> cwltool,</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> imagemagick,</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3,</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-boto,</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python3-botocore,</span>
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11
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> python3-configargparse,</span>
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12
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> python3-datrie,</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> python3-dropbox,</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> python3-flask,</span>
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13
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> python3-git,</span>
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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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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> python3-jsonschema,</span>
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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="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="plaintext"> python3-networkx,</span>
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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="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">@@ -29,6 +34,7 @@ Build-Depends: debhelper (>= 11~),</td>
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29
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> python3-wrapt,</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> python3-yaml,</span>
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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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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> r-cran-rmarkdown</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"># python3-irodsclient, # when that enters testing</span>
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32
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Standards-Version: 4.3.0</span>
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33
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/snakemake</span>
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34
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/snakemake.git</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">@@ -54,8 +60,14 @@ Depends: ${misc:Depends},</td>
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54
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> python3-setuptools,</span>
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55
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> python3-wrapt,</span>
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56
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> python3-yaml</span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">Recommends: python3-boto,</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> r-cran-rmarkdown</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">Recommends: cwltool,</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> python3-boto,</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> python3-botocore,</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> python3-dropbox,</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> python3-flask,</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> r-cran-rmarkdown,</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> imagemagick</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"># python3-irodsclient, when it enters testing</span>
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59
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">Description: pythonic workflow management system</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> Build systems like GNU Make are frequently used to create complicated</span>
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61
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"> workflows, e.g. in bioinformatics. This project aims to reduce the</span>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tests/</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#14311a7e2fde4d3f5412d248239270f0dcead73f"><strong>debian/patches/0012-reproducible-build.patch</strong></a>
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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">@@ -2,9 +2,9 @@ Description: Make the build reproducible</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Chris Lamb <lamby@debian.org></span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2019-07-15</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- snakemake<span class="idiff left right">-5.5.3</span>.orig/snakemake/report/__init__.py</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake<span class="idiff left right">-5.5.3</span>/snakemake/report/__init__.py</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">98,10 +98,12 @@</span></span><span class="idiff right"> def data_uri_from_file(file, defaultenc=</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- snakemake.orig/snakemake/report/__init__.py</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake/snakemake/report/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">100,10 +100,12 @@</span></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> def report(text, path,</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">@@ -18,9 +18,9 @@ Last-Update: 2019-07-15</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> outmime, _ = mimetypes.guess_type(path)</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> if outmime != "text/html":</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> raise ValueError("Path to report output has to be an HTML file.")</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- snakemake<span class="idiff left right">-5.5.3</span>.orig/snakemake/utils.py</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake<span class="idiff left right">-5.5.3</span>/snakemake/utils.py</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="p">@@ -189,7 +189,7 @@</span><span class="idiff left right"> def makedirs(dirnames):</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- snakemake.orig/snakemake/utils.py</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake/snakemake/utils.py</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -189,7 +189,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> def report(text, path,</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">@@ -29,7 +29,7 @@ Last-Update: 2019-07-15</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> defaultenc="utf8",</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> template=None,</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> metadata=None, **files):</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="p">@@ -233,6 +233,8 @@</span><span class="idiff left right"> def report(text, path,</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -233,6 +233,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> metadata (str): E.g. an optional author name or email address.</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> """</span>
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<li id="129f87da0c8d360881ba445e9228a00e19477a56">
<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#129f87da0c8d360881ba445e9228a00e19477a56"><strong>debian/patches/0013-remove-duplicate-keyword-argument.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From 6d013348a3501b6c183438cfb44bf78704128925 Mon Sep 17 00:00:00 2001</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Alistair Miles <alimanfoo@googlemail.com></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Date: Mon, 29 Jul 2019 14:53:04 +0000</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Subject: [PATCH] Merged in</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> alimanfoo/snakemake/Alistair-Miles/remove-duplicate-keyword-argument-1563308166092</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> (pull request #397)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">remove duplicate keyword argument</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> snakemake/remote/gfal.py | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> 1 file changed, 1 insertion(+), 1 deletion(-)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff">--- snakemake.orig/snakemake/remote/gfal.py</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake/snakemake/remote/gfal.py</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -26,7 +26,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> supports_default = True</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> allows_directories = True</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def __init__(self, *args, keep_local=False, stay_on_remote=False, is_default=False, stay_on_remote=False, retry=5, **kwargs):</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def __init__(self, *args, keep_local=False, stay_on_remote=False, is_default=False, retry=5, **kwargs):</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> super(RemoteProvider, self).__init__(*args, keep_local=keep_local, stay_on_remote=stay_on_remote, is_default=is_default, **kwargs)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> self.retry = retry</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span></pre>
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<li id="3099d3b193ee5d195e9fef4d6fc3253cd1a1d175">
<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#3099d3b193ee5d195e9fef4d6fc3253cd1a1d175"><strong>debian/patches/boto3_is_just_boto</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: In Debian, boto3 is just boto</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- snakemake.orig/snakemake/remote/S3.py</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake/snakemake/remote/S3.py</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -16,7 +16,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> # third-party modules</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import boto3</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ import boto as boto3</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import botocore</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> except ImportError as e:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> raise WorkflowError("The Python 3 package 'boto3' "</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- snakemake.orig/snakemake/remote/S3Mocked.py</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake/snakemake/remote/S3Mocked.py</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> # third-party</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import boto3</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ import boto as boto3</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> from moto import mock_s3</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> except ImportError as e:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> raise WorkflowError("The Python 3 packages 'moto' and boto3' " +</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- snakemake.orig/tests/test_static_remote/S3MockedForStaticTest.py</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake/tests/test_static_remote/S3MockedForStaticTest.py</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> # third-party</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import boto3</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ import boto as boto3</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> from moto import mock_s3</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> import filechunkio</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> except ImportError as e:</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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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">@@ -10,3 +10,5 @@</td>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"># 0010-skip-test-without-rmarkdown.patch</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">0011-fix-privacy-breach.patch</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">0012-reproducible-build.patch</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">0013-remove-duplicate-keyword-argument.patch</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">boto3_is_just_boto</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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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">@@ -6,6 +6,17 @@</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">export PYBUILD_NAME=snakemake</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export PYBUILD_DESTDIR_python3=debian/snakemake</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST_python3=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir}</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest tests/test*.py -v -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093'</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"># test_report</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"># test_ancient</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"># test_script requires conda; manually disabling conda show the need for the binary 'julia'</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"># test_default_remote requires network access</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"># test_issue634 requires conda, but passes when conda is turned off manually</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"># test_convert_to_cwl tries to build a singularity format software image from docker://quay.io/snakemake/snakemake:v5.5.4</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"># test_issue1083 tries to build a singularity format software image from docker://bash</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"># test_issue1093 fails due to conda usage; commenting that out and installing bwa produces a different ordering than desired</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">export PATH:=$(shell pybuild --print build_dir --interpreter python3 --name $(PYBUILD_NAME))/bin:$(PATH)</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">@@ -21,3 +32,6 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> PATH=$(shell pybuild --print build_dir --interpreter python3)/bin:$(PATH) \</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> PYTHONPATH=$(shell pybuild --print build_dir --interpreter python3) \</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> python3 setup.py build_sphinx</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> PYBUILD_SYSTEM=custom dh_auto_test</span></pre>
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<li id="85ccdeeb03055211183e48520592d9a93592b330">
<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#85ccdeeb03055211183e48520592d9a93592b330"><strong>debian/source/lintian-overrides</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># This is just pure test data we need to compare with</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">snakemake source: source-is-missing tests/test_report/report.html line length is *</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">snakemake source: source-is-missing tests/test_report/expected-results/report.html line length is *</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">snakemake source: source-is-missing tests/test_report/expected-results/report.html line length is *</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#9617ea0d5d1a492cd381dd6bb688b8a5cbe6512b"><strong>docs/getting_started/installation.rst</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.. getting_started-installation:</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.. <span class="idiff left right">_</span>getting_started-installation:</span>
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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">============</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Installation</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">@@ -7,6 +7,8 @@ Installation</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Snakemake is available on PyPi as well as through Bioconda and also from source code.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">You can use one of the following ways for installing Snakemake.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.. _conda-install:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Installation via Conda</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">======================</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#d0153cac95479af9bfb99b746b633bc8255bb53a"><strong>docs/index.rst</strong></a>
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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">@@ -179,6 +179,7 @@ Please consider to add your own.</td>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext"> getting_started/installation</span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="plaintext"> getting_started/examples</span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext"> tutorial/tutorial</span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> tutorial/short</span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext">.. toctree::</span>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#a64f4e86841a3aed0cd5f5ec9d71431086ea0014"><strong>docs/tutorial/advanced.rst</strong></a>
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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">@@ -203,7 +203,7 @@ We modify the rule ``bwa_map`` accordingly:</td>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="plaintext"> initialization to the DAG phase. In contrast to input functions, these can</span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="plaintext"> optionally take additional arguments ``input``, ``output``, ``threads``, and ``resources``.</span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext">Similar to input and output files, ``params`` can be accessed from the shell command <span class="idiff left right">or the Python based ``run`` block (see :ref:`tutorial-repor</span>t`).</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">Similar to input and output files, ``params`` can be accessed from the shell command <span class="idiff left right">the Python based ``run`` block, or the script directive (see :ref:`tutorial-scrip</span>t`).</span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="plaintext">Exercise</span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext">........</span>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#7f695df9a93bb6d2f47c562fd1282181e830528b"><strong>docs/tutorial/basics.rst</strong></a>
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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">@@ -365,8 +365,10 @@ Exercise</td>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="plaintext"> :align: center</span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext">.. _tutorial-script:</span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="plaintext">Step 6: Using custom scripts</span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="plaintext">::::::::::::::::::::</span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext">::::::::::::::::::::<span class="idiff left right">::::::::</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="plaintext">Usually, a workflow not only consists of invoking various tools, but also contains custom code to e.g. calculate summary statistics or create plots.</span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="plaintext">While Snakemake also allows you to directly :ref:`write Python code inside a rule <.. _snakefiles-rules>`_, it is usually reasonable to move such logic into separate scripts.</span>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#54c391de2500e0856c23737daf64f9d931569110"><strong>environment.yml</strong></a>
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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">@@ -31,3 +31,4 @@ dependencies:</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">xorg-libxrender</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">xorg-libxpm</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gitpython</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pygments</span></span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#c2acba86d5ef7b186a3f54c5fcbfeeb889e18738"><strong>misc/vim/syntax/snakemake.vim</strong></a>
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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">@@ -26,25 +26,29 @@ source $VIMRUNTIME/syntax/python.vim</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" XXX N.B. several of the new defs are missing from this table i.e.</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" subworkflow, touch etc</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">"</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" rule = "rule" (identifier | "") ":" ruleparams</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" include = "include:" stringliteral</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" workdir = "workdir:" stringliteral</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" ni = NEWLINE INDENT</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" ruleparams = [ni input] [ni output] [ni params] [ni message] [ni threads] [ni (run | shell)] NEWLINE snakemake</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" input = "input" ":" parameter_list</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" output = "output" ":" parameter_list</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" params = "params" ":" parameter_list</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" message = "message" ":" stringliteral</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" threads = "threads" ":" integer</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" resources = "resources" ":" parameter_list</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" version = "version" ":" statement</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" run = "run" ":" ni statement</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" shell = "shell" ":" stringliteral</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" rule = "rule" (identifier | "") ":" ruleparams</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" include = "include:" stringliteral</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" workdir = "workdir:" stringliteral</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" ni = NEWLINE INDENT</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" ruleparams = [ni input] [ni output] [ni params] [ni message] [ni threads] [ni (run | shell)] NEWLINE snakemake</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" input = "input" ":" parameter_list</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" output = "output" ":" parameter_list</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" params = "params" ":" parameter_list</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" message = "message" ":" stringliteral</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" threads = "threads" ":" integer</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" resources = "resources" ":" parameter_list</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" version = "version" ":" statement</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" run = "run" ":" ni statement</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" shell = "shell" ":" stringliteral</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" singularity = "singularity" ":" stringliteral</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" conda = "conda" ":" stringliteral</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="viml"><span class="c" style="color: #998; font-style: italic;">" shadow = "shadow" ":" stringliteral</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="viml"></span>
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43
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="viml"></span>
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44
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="viml"><span class="k" style="font-weight: 600;">syn</span> keyword pythonStatement include workdir onsuccess onerror</span>
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45
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="viml"><span class="k" style="font-weight: 600;">syn</span> keyword pythonStatement ruleorder localrules configfile</span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="viml"><span class="k" style="font-weight: 600;">syn</span> keyword pythonStatement touch protected temp wrapper</span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="viml"><span class="k" style="font-weight: 600;">syn</span> keyword pythonStatement input output params message threads resources</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="viml"><span class="k" style="font-weight: 600;">syn</span> keyword pythonStatement touch protected temp wrapper<span class="idiff left right"> conda shadow</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="viml"><span class="k" style="font-weight: 600;">syn</span> keyword pythonStatement input output params message threads resources<span class="idiff left right"> singularity</span></span>
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48
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="viml"><span class="k" style="font-weight: 600;">syn</span> keyword pythonStatement version run <span class="k" style="font-weight: 600;">shell</span> benchmark snakefile log <span class="k" style="font-weight: 600;">script</span></span>
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49
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="viml"><span class="k" style="font-weight: 600;">syn</span> keyword pythonStatement rule subworkflow nextgroup<span class="p">=</span>pythonFunction skipwhite</span>
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50
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="viml"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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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">@@ -49,7 +49,7 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'wrapt'</span><span class="p">,</span> <span class="s" style="color: #d14;">'requests'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ratelimiter'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pyyaml'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">'configargparse'</span><span class="p">,</span> <span class="s" style="color: #d14;">'appdirs'</span><span class="p">,</span> <span class="s" style="color: #d14;">'datrie'</span><span class="p">,</span> <span class="s" style="color: #d14;">'jsonschema'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">'docutils'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gitpython'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">extras_require</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"reports"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'jinja2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'networkx'</span><span class="p">]},</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">extras_require</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"reports"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'jinja2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'networkx'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'pygments'</span></span><span class="p">]},</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"Development Status :: 5 - Production/Stable"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Environment :: Console"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="s" style="color: #d14;">"Intended Audience :: Science/Research"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#5e16cbeea010f59dbef52f8950f4873c94f39c7e"><strong>snakemake/_version.py</strong></a>
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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">@@ -23,9 +23,9 @@ def get_keywords():</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># setup.py/versioneer.py will grep for the variable names, so they must</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># each be defined on a line of their own. _version.py will just call</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># get_keywords().</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (<span class="idiff left right">HEAD -> master, tag: v5.5.3</span>)"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">66c61c139e1f439e3f78c09df97927ad54363cc3</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2019-07-<span class="idiff left right">11 18:27:18</span> +0200"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (<span class="idiff left right">tag: v5.5.4</span>)"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">a98c6317d6269c6b339bdca70521bbeb155ba90f</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2019-07-<span class="idiff left right">21 09:16:33</span> +0200"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"refnames"</span><span class="p">:</span> <span class="n" style="color: #333;">git_refnames</span><span class="p">,</span> <span class="s" style="color: #d14;">"full"</span><span class="p">:</span> <span class="n" style="color: #333;">git_full</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">git_date</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">keywords</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#6c195c1be80e4ad60b55a5a06c27411c43bbc217"><strong>snakemake/logging.py</strong></a>
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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">@@ -344,7 +344,7 @@ class Logger:</td>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">format_dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">,</span> <span class="n" style="color: #333;">omit_keys</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">omit_values</span><span class="o" style="font-weight: 600;">=</span><span class="p">[]):</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">", "</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"{}={}"</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;">name</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">value</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">", "</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"{}={}"</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;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</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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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</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;">omit_keys</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">value</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;">omit_values</span><span class="p">)</span></span>
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350
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#3065d4749c6410564a20007bd7748abfda7699f6"><strong>snakemake/report/__init__.py</strong></a>
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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">@@ -25,6 +25,7 @@ from docutils.parsers.rst.directives.images import Image, Figure</td>
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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;">docutils.parsers.rst</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">directives</span></span>
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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;">docutils.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">publish_file</span><span class="p">,</span> <span class="n" style="color: #333;">publish_parts</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">script</span><span class="p">,</span> <span class="n" style="color: #333;">wrapper</span></span>
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<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;">snakemake.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="nb" style="color: #0086b3;">format</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.logging</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">logger</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.io</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">is_flagged</span><span class="p">,</span> <span class="n" style="color: #333;">get_flag_value</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">@@ -32,6 +33,7 @@ from snakemake.exceptions import WorkflowError</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.script</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Snakemake</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.common</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">num_if_possible</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">logging</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">EmbeddedMixin</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</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">@@ -183,9 +185,11 @@ class Category:</td>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">RuleRecord</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC189" 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;">job</span><span class="p">,</span> <span class="n" style="color: #333;">job_rec</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">yaml</span></span>
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<pre style="margin: 0;"> <span id="LC191" 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;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">job_rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rule</span></span>
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<pre style="margin: 0;">+<span id="LC192" 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;">_rule</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;">rule</span></span>
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189
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<pre style="margin: 0;"> <span id="LC193" 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;">singularity_img_url</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">job_rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">singularity_img_url</span></span>
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190
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<pre style="margin: 0;"> <span id="LC194" 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;">conda_env</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC195" 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;">_conda_env_raw</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" style="width: 35px; color: rgba(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">@@ -196,6 +200,32 @@ class RuleRecord:</td>
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196
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200
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<pre style="margin: 0;"> <span id="LC200" 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;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">job_rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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197
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</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>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">code</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC204" 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="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pygments.lexers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_lexer_by_name</span></span>
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<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pygments.formatters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">HtmlFormatter</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pygments</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">highlight</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span><span class="s" style="color: #d14;">"Python package pygments must be installed to create reports."</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shellcmd</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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<td class="diff-line-num new new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">source</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;">_rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shellcmd</span></span>
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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"bash"</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">script</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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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
215
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<pre style="margin: 0;">+<span id="LC215" 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;">"Loading script code for rule {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</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;">name</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_source</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;">_rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">script</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;">_rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basedir</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wrapper</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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<td class="diff-line-num new new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
219
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<pre style="margin: 0;">+<span id="LC219" 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;">"Loading wrapper code for rule {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</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;">name</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_source</span><span class="p">(</span><span class="n" style="color: #333;">wrapper</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_script</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;">_rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wrapper</span><span class="p">,</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;">_rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">workflow</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wrapper_prefix</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">()</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">lexer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_lexer_by_name</span><span class="p">(</span><span class="n" style="color: #333;">language</span><span class="p">)</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">highlight</span><span class="p">(</span><span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">lexer</span><span class="p">,</span> <span class="n" style="color: #333;">HtmlFormatter</span><span class="p">(</span><span class="n" style="color: #333;">linenos</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">cssclass</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"source"</span><span class="p">,</span> <span class="n" style="color: #333;">wrapcode</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">pygments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ClassNotFound</span><span class="p">:</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<pre><code>source</code></pre>"</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"></span>
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199
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">job_rec</span><span class="p">):</span></span>
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200
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230
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<pre style="margin: 0;"> <span id="LC230" 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;">n_jobs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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201
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<pre style="margin: 0;"> <span id="LC231" 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;">output</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;">job_rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="206" style="width: 35px; color: rgba(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">@@ -206,8 +236,27 @@ class RuleRecord:</td>
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206
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236
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<pre style="margin: 0;"> <span id="LC236" 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;">singularity_img_url</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">singularity_img_url</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"></span>
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208
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ConfigfileRecord</span><span class="p">:</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" 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;">configfile</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC241" 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;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">configfile</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> </span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">code</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pygments.lexers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_lexer_by_name</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pygments.formatters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">HtmlFormatter</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pygments</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">highlight</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span><span class="s" style="color: #d14;">"Python package pygments must be installed to create reports."</span><span class="p">)</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"yaml"</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".yaml"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".yml"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"json"</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">lexer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_lexer_by_name</span><span class="p">(</span><span class="n" style="color: #333;">language</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
253
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<pre style="margin: 0;">+<span id="LC253" 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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">highlight</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(),</span> <span class="n" style="color: #333;">lexer</span><span class="p">,</span> <span class="n" style="color: #333;">HtmlFormatter</span><span class="p">(</span><span class="n" style="color: #333;">linenos</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">cssclass</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"source"</span><span class="p">,</span> <span class="n" style="color: #333;">wrapcode</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"></span>
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209
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">JobRecord</span><span class="p">:</span></span>
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210
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<pre style="margin: 0;"> <span id="LC258" 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>
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<pre style="margin: 0;">+<span id="LC259" 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;">job</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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211
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260
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<pre style="margin: 0;"> <span id="LC260" 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;">rule</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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212
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261
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<pre style="margin: 0;"> <span id="LC261" 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;">starttime</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;">maxsize</span></span>
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213
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262
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<pre style="margin: 0;"> <span id="LC262" 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;">endtime</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="226" style="width: 35px; color: rgba(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="275" style="width: 35px; color: rgba(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">@@ -226,6 +275,8 @@ class FileRecord:</td>
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226
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275
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<pre style="margin: 0;"> <span id="LC275" 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;">mime</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;">mime_from_file</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;">path</span><span class="p">)</span></span>
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227
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</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>
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228
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<pre style="margin: 0;"> <span id="LC277" 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;">job</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">job</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" 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;">wildcards</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format_wildcards</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wildcards</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC279" 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;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format_dict</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">params</span><span class="p">)</span></span>
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229
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280
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<pre style="margin: 0;"> <span id="LC280" 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;">png_uri</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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230
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281
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<pre style="margin: 0;"> <span id="LC281" 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;">category</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">category</span></span>
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231
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_img</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="419" style="width: 35px; color: rgba(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="470" style="width: 35px; color: rgba(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">@@ -419,6 +470,7 @@ def auto_report(dag, path):</td>
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419
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470
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="python"> <span class="n" style="color: #333;">rule</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">meta</span><span class="p">[</span><span class="s" style="color: #d14;">"rule"</span><span class="p">]</span></span>
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420
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471
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python"> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">records</span><span class="p">[(</span><span class="n" style="color: #333;">job_hash</span><span class="p">,</span> <span class="n" style="color: #333;">rule</span><span class="p">)]</span></span>
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421
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472
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rule</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;">rec</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;">job</span></span>
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422
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474
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">starttime</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">starttime</span><span class="p">,</span> <span class="n" style="color: #333;">meta</span><span class="p">[</span><span class="s" style="color: #d14;">"starttime"</span><span class="p">])</span></span>
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423
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475
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endtime</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endtime</span><span class="p">,</span> <span class="n" style="color: #333;">meta</span><span class="p">[</span><span class="s" style="color: #d14;">"endtime"</span><span class="p">])</span></span>
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476
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">conda_env_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="446" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -446,7 +498,7 @@ def auto_report(dag, path):</td>
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446
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># prepare per-rule information</span></span>
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447
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">rules</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">)</span></span>
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448
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500
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">records</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>
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449
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="python"> <span class="n" style="color: #333;">rule</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RuleRecord</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python"> <span class="n" style="color: #333;">rule</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RuleRecord</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">rec</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">job</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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450
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rule</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;">rules</span><span class="p">:</span></span>
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451
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">rules</span><span class="p">[</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rule</span><span class="p">]</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;">rule</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</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">@@ -462,6 +514,8 @@ def auto_report(dag, path):</td>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># rulegraph</span></span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">rulegraph</span><span class="p">,</span> <span class="n" style="color: #333;">xmax</span><span class="p">,</span> <span class="n" style="color: #333;">ymax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rulegraph_d3_spec</span><span class="p">(</span><span class="n" style="color: #333;">dag</span><span class="p">)</span></span>
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516
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># configfiles</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"> <span class="n" style="color: #333;">configfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">ConfigfileRecord</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dag</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">workflow</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">configfiles</span><span class="p">]</span></span>
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465
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519
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python"> <span class="n" style="color: #333;">seen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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467
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521
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">seen</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">target</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">res</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">res</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cat</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">target</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;">seen</span><span class="p">]</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="553" style="width: 35px; color: rgba(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">@@ -499,11 +553,17 @@ def auto_report(dag, path):</td>
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499
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python"> <span class="n" style="color: #333;">now</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="nb" style="color: #0086b3;">format</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ctime</span><span class="p">(),</span> <span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tzname</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="python"> <span class="n" style="color: #333;">results_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">res</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cat</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pygments.formatters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">HtmlFormatter</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span><span class="s" style="color: #d14;">"Python package pygments must be installed to create reports."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="python"></span>
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># render HTML</span></span>
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562
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="python"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">env</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_template</span><span class="p">(</span><span class="s" style="color: #d14;">"report.html"</span><span class="p">)</span></span>
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504
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563
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<pre style="margin: 0;"> <span id="LC563" 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;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">,</span> <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"utf-8"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">out</span><span class="p">:</span></span>
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505
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="python"> <span class="n" style="color: #333;">out</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;">template</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">render</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">results</span><span class="p">,</span></span>
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506
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python"> <span class="n" style="color: #333;">results_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">results_size</span><span class="p">,</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"> <span class="n" style="color: #333;">configfiles</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">configfiles</span><span class="p">,</span></span>
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507
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python"> <span class="n" style="color: #333;">text</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">text</span><span class="p">,</span></span>
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508
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="python"> <span class="n" style="color: #333;">rulegraph_nodes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rulegraph</span><span class="p">[</span><span class="s" style="color: #d14;">"nodes"</span><span class="p">],</span></span>
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509
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="python"> <span class="n" style="color: #333;">rulegraph_links</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rulegraph</span><span class="p">[</span><span class="s" style="color: #d14;">"links"</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">@@ -513,5 +573,6 @@ def auto_report(dag, path):</td>
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513
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573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="n" style="color: #333;">timeline</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">timeline</span><span class="p">,</span></span>
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574
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">rules</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">rec</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">recs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rules</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">recs</span><span class="p">],</span></span>
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515
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575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__version__</span><span class="p">,</span></span>
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516
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">now</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">now</span><span class="p">))</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="python"> <span class="n" style="color: #333;">now</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">now</span><span class="p">,</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="python"> <span class="n" style="color: #333;">pygments_css</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">HtmlFormatter</span><span class="p">(</span><span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"trac"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_style_defs</span><span class="p">(</span><span class="s" style="color: #d14;">'.source'</span><span class="p">)))</span></span>
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517
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578
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<pre style="margin: 0;"> <span id="LC578" 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;">"Report created."</span><span class="p">)</span></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">@@ -11,7 +11,8 @@</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="html"> <span class="c" style="color: #998; font-style: italic;"><!-- Bootstrap CSS --></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="html"> <span class="nt" style="color: #000080;"><style></span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="py">https</span><span class="p">://</span><span class="n" style="color: #333;">stackpath</span><span class="p">.</span><span class="n" style="color: #333;">bootstrapcdn</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">bootstrap</span><span class="p">/</span><span class="m" style="color: #099;">4.1.1</span><span class="p">/</span><span class="n" style="color: #333;">css</span><span class="p">/</span><span class="n" style="color: #333;">bootstrap</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">.</span><span class="n" style="color: #333;">css</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"|</span><span class="n" style="color: #333;">get_resource_as_string</span> <span class="p">}</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span><span class="nt" style="color: #000080;"></style></span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="html"> <span class="nt" style="color: #000080;"><style></span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="py">https</span><span class="p">://</span><span class="n" style="color: #333;">cdnjs</span><span class="p">.</span><span class="n" style="color: #333;">cloudflare</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">ajax</span><span class="p">/</span><span class="n" style="color: #333;">libs</span><span class="p">/</span><span class="n" style="color: #333;">ekko-lightbox</span><span class="p">/</span><span class="m" style="color: #099;">5.3.0</span><span class="p">/</span><span class="n" style="color: #333;">ekko-lightbox</span><span class="p">.</span><span class="n" style="color: #333;">css</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"|</span><span class="n" style="color: #333;">get_resource_as_string</span> <span class="p">}</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span><span class="nt" style="color: #000080;"></style></span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="html"> <span class="nt" style="color: #000080;"><style></span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="py">https</span><span class="p">://</span><span class="n" style="color: #333;">cdn</span><span class="p">.</span><span class="n" style="color: #333;">datatables</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">v</span><span class="p">/</span><span class="n" style="color: #333;">bs4</span><span class="p">/</span><span class="n" style="color: #333;">dt-1</span><span class="m" style="color: #099;">.10.18</span><span class="p">/</span><span class="n" style="color: #333;">r-2</span><span class="m" style="color: #099;">.2.2</span><span class="p">/</span><span class="n" style="color: #333;">datatables</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">.</span><span class="n" style="color: #333;">css</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"|</span><span class="n" style="color: #333;">get_resource_as_string</span> <span class="p">}</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span><span class="nt" style="color: #000080;"></style></span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="html"> <span class="nt" style="color: #000080;"><style></span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="py">https</span><span class="p">://</span><span class="n" style="color: #333;">cdn</span><span class="p">.</span><span class="n" style="color: #333;">datatables</span><span class="p">.</span><span class="n" style="color: #333;">net</span><span class="p">/</span><span class="n" style="color: #333;">v</span><span class="p">/</span><span class="n" style="color: #333;">bs4</span><span class="p">/</span><span class="n" style="color: #333;">dt-1</span><span class="m" style="color: #099;">.10.18</span><span class="p">/</span><span class="n" style="color: #333;">r-2</span><span class="m" style="color: #099;">.2.2</span><span class="p">/</span><span class="n" style="color: #333;">sl-1</span><span class="m" style="color: #099;">.3.0</span><span class="p">/</span><span class="n" style="color: #333;">datatables</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">.</span><span class="n" style="color: #333;">css</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"|</span><span class="n" style="color: #333;">get_resource_as_string</span> <span class="p">}</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span><span class="nt" style="color: #000080;"></style></span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="html"> <span class="nt" style="color: #000080;"><style></span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pygments_css|safe</span> <span class="p">}</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span><span class="nt" style="color: #000080;"></style></span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="html"> <span class="c" style="color: #998; font-style: italic;"><!-- Custom styles for this template --></span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="html"> <span class="nt" style="color: #000080;"><style></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">@@ -203,6 +204,37 @@</td>
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="html"> <span class="nc" style="color: #458; font-weight: 600;">.navbar</span> <span class="p">{</span></span>
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="html"> <span class="nl">opacity</span><span class="p">:</span> <span class="m" style="color: #099;">0.8</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="html"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="html"></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="html"> <span class="nc" style="color: #458; font-weight: 600;">.source</span> <span class="p">{</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="html"> <span class="nl">background</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">none</span> <span class="cp" style="color: #999; font-weight: 600;">!important</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="html"> <span class="p">}</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="html"></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="html"> <span class="nt" style="color: #000080;">table</span><span class="nc" style="color: #458; font-weight: 600;">.dataTable</span> <span class="nt" style="color: #000080;">tbody</span> <span class="nt" style="color: #000080;">tr</span><span class="nc" style="color: #458; font-weight: 600;">.selected</span><span class="o" style="font-weight: 600;">,</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="html"> <span class="nt" style="color: #000080;">table</span><span class="nc" style="color: #458; font-weight: 600;">.dataTable</span> <span class="nt" style="color: #000080;">tbody</span> <span class="nt" style="color: #000080;">th</span><span class="nc" style="color: #458; font-weight: 600;">.selected</span><span class="o" style="font-weight: 600;">,</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="html"> <span class="nt" style="color: #000080;">table</span><span class="nc" style="color: #458; font-weight: 600;">.dataTable</span> <span class="nt" style="color: #000080;">tbody</span> <span class="nt" style="color: #000080;">td</span><span class="nc" style="color: #458; font-weight: 600;">.selected</span> <span class="p">{</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="html"> <span class="nl">color</span><span class="p">:</span> <span class="no" style="color: #008080;">black</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="html"> <span class="p">}</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="html"> <span class="nt" style="color: #000080;">table</span><span class="nc" style="color: #458; font-weight: 600;">.dataTable</span> <span class="nt" style="color: #000080;">tbody</span> <span class="nt" style="color: #000080;">tr</span><span class="nc" style="color: #458; font-weight: 600;">.selected</span> <span class="nt" style="color: #000080;">td</span><span class="nd">:first-of-type</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="html"> <span class="nl">font-weight</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bold</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="html"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="html"></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="html"> <span class="nt" style="color: #000080;">table</span><span class="nc" style="color: #458; font-weight: 600;">.dataTable</span> <span class="nt" style="color: #000080;">tbody</span> <span class="nt" style="color: #000080;">tr</span><span class="nc" style="color: #458; font-weight: 600;">.selected</span> <span class="nt" style="color: #000080;">td</span> <span class="p">{</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="html"> <span class="nl">border-top</span><span class="p">:</span> <span class="m" style="color: #099;">1px</span> <span class="nb" style="color: #0086b3;">solid</span> <span class="m" style="color: #099;">#007bff</span><span class="p">;</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="html"> <span class="nl">border-bottom</span><span class="p">:</span> <span class="m" style="color: #099;">1px</span> <span class="nb" style="color: #0086b3;">solid</span> <span class="m" style="color: #099;">#007bff</span><span class="p">;</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="html"> <span class="p">}</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="html"></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="html"> <span class="nt" style="color: #000080;">table</span><span class="nc" style="color: #458; font-weight: 600;">.dataTable</span> <span class="nt" style="color: #000080;">tbody</span> <span class="o" style="font-weight: 600;">></span> <span class="nt" style="color: #000080;">tr</span><span class="nc" style="color: #458; font-weight: 600;">.selected</span><span class="o" style="font-weight: 600;">,</span> </span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="html"> <span class="nt" style="color: #000080;">table</span><span class="nc" style="color: #458; font-weight: 600;">.dataTable</span> <span class="nt" style="color: #000080;">tbody</span> <span class="o" style="font-weight: 600;">></span> <span class="nt" style="color: #000080;">tr</span> <span class="o" style="font-weight: 600;">></span> <span class="nc" style="color: #458; font-weight: 600;">.selected</span> <span class="p">{</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="html"> <span class="nl">background-color</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">transparent</span><span class="p">;</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="html"> <span class="p">}</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="html"></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="html"> <span class="nt" style="color: #000080;">table</span><span class="nc" style="color: #458; font-weight: 600;">.dataTable</span> <span class="nt" style="color: #000080;">tbody</span> <span class="nt" style="color: #000080;">tr</span><span class="nc" style="color: #458; font-weight: 600;">.selected</span> <span class="nt" style="color: #000080;">a</span><span class="o" style="font-weight: 600;">,</span> </span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="html"> <span class="nt" style="color: #000080;">table</span><span class="nc" style="color: #458; font-weight: 600;">.dataTable</span> <span class="nt" style="color: #000080;">tbody</span> <span class="nt" style="color: #000080;">th</span><span class="nc" style="color: #458; font-weight: 600;">.selected</span> <span class="nt" style="color: #000080;">a</span><span class="o" style="font-weight: 600;">,</span> </span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="html"> <span class="nt" style="color: #000080;">table</span><span class="nc" style="color: #458; font-weight: 600;">.dataTable</span> <span class="nt" style="color: #000080;">tbody</span> <span class="nt" style="color: #000080;">td</span><span class="nc" style="color: #458; font-weight: 600;">.selected</span> <span class="nt" style="color: #000080;">a</span> <span class="p">{</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="html"> <span class="nl">color</span><span class="p">:</span> <span class="m" style="color: #099;">#007bff</span><span class="p">;</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="html"> <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">@@ -213,7 +245,7 @@</td>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="html"> <span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"info"</span><span class="nt" style="color: #000080;">></span>Loading {{ results_size|filesizeformat }}. For large reports, this can take a while.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="html"> <span class="nt" style="color: #000080;"><nav</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"navbar <span class="idiff left right">navbar-dark fixed-top</span> bg-dark flex-md-nowrap p-0 shadow"</span><span class="nt" style="color: #000080;">></span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="html"> <span class="nt" style="color: #000080;"><nav</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"navbar <span class="idiff left right">fixed-top navbar-dark</span> bg-dark flex-md-nowrap p-0 shadow"</span><span class="nt" style="color: #000080;">></span></span>
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="html"> <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"navbar-brand col-sm-3 col-md-2 mr-0"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#"</span><span class="nt" style="color: #000080;">></span>Snakemake Report<span class="nt" style="color: #000080;"></a></span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="html"> <span class="nt" style="color: #000080;"><ul</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"nav navbar-nav navbar-right"</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"padding-right: 10px;"</span><span class="nt" style="color: #000080;">></span></span>
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="html"> <span class="nt" style="color: #000080;"><li</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"text-white"</span><span class="nt" style="color: #000080;">></span>{{ now }}<span class="nt" style="color: #000080;"></li></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">@@ -229,7 +261,7 @@</td>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="html"> <span class="nt" style="color: #000080;"><ul</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"nav flex-column"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="html"> <span class="nt" style="color: #000080;"><li</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"nav-item"</span><span class="nt" style="color: #000080;">></span></span>
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="html"> <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"nav-link active"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">data-feather=</span><span class="s" style="color: #d14;">"<span class="idiff left right">home</span>"</span><span class="nt" style="color: #000080;">></span></span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">data-feather=</span><span class="s" style="color: #d14;">"<span class="idiff left right">git-pull-request</span>"</span><span class="nt" style="color: #000080;">></span></span></span>
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="html"> Workflow <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"sr-only"</span><span class="nt" style="color: #000080;">></span>(current)<span class="nt" style="color: #000080;"></span></span></span>
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="html"> <span class="nt" style="color: #000080;"></li></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">@@ -239,6 +271,14 @@</td>
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="html"> Statistics</span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="html"> <span class="nt" style="color: #000080;"></a></span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="html"> <span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="html"> {% if configfiles %}</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="html"> <span class="nt" style="color: #000080;"><li</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"nav-item"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="html"> <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"nav-link"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#configuration"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">data-feather=</span><span class="s" style="color: #d14;">"settings"</span><span class="nt" style="color: #000080;">></span></span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="html"> Configuration</span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="html"> <span class="nt" style="color: #000080;"></a></span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="html"> <span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="html"> {% endif %}</span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="html"> <span class="nt" style="color: #000080;"><li</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"nav-item"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="html"> <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"nav-link"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#rules"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">data-feather=</span><span class="s" style="color: #d14;">"list"</span><span class="nt" style="color: #000080;">></span></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">@@ -273,7 +313,11 @@</td>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="html"> <span class="nt" style="color: #000080;"><p></span>Detailed software versions can be found under <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#rules"</span><span class="nt" style="color: #000080;">></span>Rules<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"rulegraph"</span><span class="nt" style="color: #000080;">></div></span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"row justify-content-center"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"col-xs-6"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"rulegraph"</span><span class="nt" style="color: #000080;">></div></span></span>
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"d-flex justify-content-between flex-wrap flex-md-nowrap align-items-center pt-3 pb-2 mb-3 border-bottom"</span><span class="nt" style="color: #000080;">></span></span>
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279
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="html"> <span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"results"</span><span class="nt" style="color: #000080;">></span>Results<span class="nt" style="color: #000080;"></h2></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="298" style="width: 35px; color: rgba(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="342" style="width: 35px; color: rgba(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">@@ -298,6 +342,7 @@</td>
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298
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>File<span class="nt" style="color: #000080;"></th></span></span>
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299
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>Size<span class="nt" style="color: #000080;"></th></span></span>
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300
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>Description<span class="nt" style="color: #000080;"></th></span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>Job properties<span class="nt" style="color: #000080;"></th></span></span>
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301
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></th></span></span>
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302
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="html"> <span class="nt" style="color: #000080;"></tr></span></span>
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303
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="html"> <span class="nt" style="color: #000080;"></thead></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="309" style="width: 35px; color: rgba(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">@@ -309,6 +354,25 @@</td>
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309
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354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="html"> <span class="nt" style="color: #000080;"></th></span></span>
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310
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="html"> <span class="nt" style="color: #000080;"><td</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"white-space:nowrap;"</span><span class="nt" style="color: #000080;">></span>{{ res.size|filesizeformat }}<span class="nt" style="color: #000080;"></td></span></span>
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311
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="html"> <span class="nt" style="color: #000080;"><td></span>{{ res.caption }}<span class="nt" style="color: #000080;"></td></span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="html"> <span class="nt" style="color: #000080;"><td></span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="html"> <span class="nt" style="color: #000080;"><table</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"table table-sm table-borderless"</span><span class="nt" style="color: #000080;">></span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="html"> <span class="nt" style="color: #000080;"><tbody></span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="html"> <span class="nt" style="color: #000080;"><tr></span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>Rule<span class="nt" style="color: #000080;"></th><td><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"rule"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"javascript:void(0)"</span><span class="nt" style="color: #000080;">></span>{{ res.job.rule }}<span class="nt" style="color: #000080;"></a></td></span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="html"> <span class="nt" style="color: #000080;"></tr></span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="html"> {% if res.wildcards %}</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="html"> <span class="nt" style="color: #000080;"><tr></span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>Wildcards<span class="nt" style="color: #000080;"></th><td></span>{{ res.wildcards }}<span class="nt" style="color: #000080;"></td></span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="html"> <span class="nt" style="color: #000080;"></tr></span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="html"> {% endif %}</span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="html"> {% if res.params %}</span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="html"> <span class="nt" style="color: #000080;"><tr></span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>Params<span class="nt" style="color: #000080;"></th><td></span>{{ res.params }}<span class="nt" style="color: #000080;"></td></span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="html"> {% endif %}</span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="html"> <span class="nt" style="color: #000080;"></table></span></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="html"> <span class="nt" style="color: #000080;"><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"preview"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"{{ res.id }}-preview"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="html"> <span class="nt" style="color: #000080;"></td></span></span>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="html"> <span class="nt" style="color: #000080;"></tr></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">@@ -325,8 +389,42 @@</td>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="html"> <span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"stats"</span><span class="nt" style="color: #000080;">></span>Statistics<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="html"> <span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="html"> If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.</span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"runtimes"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"plot"</span><span class="nt" style="color: #000080;">></div></span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"timeline"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"plot"</span><span class="nt" style="color: #000080;">></div></span></span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"row justify-content-center"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"col-xs-6"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"runtimes"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"plot"</span><span class="nt" style="color: #000080;">></div></span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"col-xs-6"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"timeline"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"plot"</span><span class="nt" style="color: #000080;">></div></span></span>
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398
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="html"> {% if configfiles %}</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"d-flex justify-content-between flex-wrap flex-md-nowrap align-items-center pt-3 pb-2 mb-3 border-bottom"</span><span class="nt" style="color: #000080;">></span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="html"> <span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"configuration"</span><span class="nt" style="color: #000080;">></span>Configuration<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="html"> <span class="nt" style="color: #000080;"><table</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"table"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>File<span class="nt" style="color: #000080;"></th></span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>Code<span class="nt" style="color: #000080;"></th></span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="html"> {% for configfile in configfiles %}</span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="html"> <span class="nt" style="color: #000080;"><tr></span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="html"> <span class="nt" style="color: #000080;"><td></span>{{ configfile.name }}<span class="nt" style="color: #000080;"></td></span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="html"> <span class="nt" style="color: #000080;"><td></span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="html"> <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">data-toggle=</span><span class="s" style="color: #d14;">"collapse"</span> <span class="na" style="color: #008080;">role=</span><span class="s" style="color: #d14;">"button"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#configfile-{{ configfile.id }}"</span> <span class="na" style="color: #008080;">aria-expanded=</span><span class="s" style="color: #d14;">"false"</span> <span class="na" style="color: #008080;">aria-controls=</span><span class="s" style="color: #d14;">"collapse-env"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">data-feather=</span><span class="s" style="color: #d14;">"plus-circle"</span><span class="nt" style="color: #000080;">></span></a></span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"collapse"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"configfile-{{ configfile.id }}"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="html"> {{ configfile.code()|safe }}</span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="html"> {% endfor %}</span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="html"> {% endif %}</span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"d-flex justify-content-between flex-wrap flex-md-nowrap align-items-center pt-3 pb-2 mb-3 border-bottom"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="html"> <span class="nt" style="color: #000080;"><h2</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"rules"</span><span class="nt" style="color: #000080;">></span>Rules<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="html"> <span class="nt" style="color: #000080;"></div></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">@@ -338,6 +436,7 @@</td>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>Output<span class="nt" style="color: #000080;"></th></span></span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>Singularity<span class="nt" style="color: #000080;"></th></span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>Conda environment<span class="nt" style="color: #000080;"></th></span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="html"> <span class="nt" style="color: #000080;"><th></span>Code<span class="nt" style="color: #000080;"></th></span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="html"> <span class="nt" style="color: #000080;"></tr></span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="html"> <span class="nt" style="color: #000080;"></thead></span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="html"> <span class="nt" style="color: #000080;"><tbody></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">@@ -368,6 +467,14 @@</td>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="html"> {% endif %}</span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="html"> <span class="nt" style="color: #000080;"></td></span></span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="html"> <span class="nt" style="color: #000080;"><td></span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="html"> {% if rule.code is not none %}</span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="html"> <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">data-toggle=</span><span class="s" style="color: #d14;">"collapse"</span> <span class="na" style="color: #008080;">role=</span><span class="s" style="color: #d14;">"button"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#code-{{ rule.id }}"</span> <span class="na" style="color: #008080;">aria-expanded=</span><span class="s" style="color: #d14;">"false"</span> <span class="na" style="color: #008080;">aria-controls=</span><span class="s" style="color: #d14;">"collapse-env"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">data-feather=</span><span class="s" style="color: #d14;">"plus-circle"</span><span class="nt" style="color: #000080;">></span></a></span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"collapse"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"code-{{ rule.id }}"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="html"> {{ rule.code()|safe }}</span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="html"> {% endif %}</span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="html"> <span class="nt" style="color: #000080;"></tr></span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="html"> {% endfor %}</span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="html"> <span class="nt" style="color: #000080;"></tbody></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">@@ -378,17 +485,18 @@</td>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="html"> <span class="c" style="color: #998; font-style: italic;"><!-- Optional JavaScript --></span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="html"> <span class="c" style="color: #998; font-style: italic;"><!-- jQuery first, then Popper.js, then Bootstrap JS --></span></span>
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.<span class="idiff left right">slim.</span>min.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.3/umd/popper.min.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://cdnjs.cloudflare.com/ajax/libs/vega-embed/<span class="idiff left right">3.13.2</span>/vega-embed.min.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://cdnjs.cloudflare.com/ajax/libs/vega/<span class="idiff left right">5.4.0</span>/vega.min.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://cdnjs.cloudflare.com/ajax/libs/vega-lite/<span class="idiff left right">3.3.0</span>/vega-lite.min.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://cdnjs.cloudflare.com/ajax/libs/vega-embed/<span class="idiff left right">4.2.1</span>/vega-embed.min.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://cdnjs.cloudflare.com/ajax/libs/feather-icons/4.7.3/feather.min.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://cdnjs.cloudflare.com/ajax/libs/ekko-lightbox/5.3.0/ekko-lightbox.min.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://raw.githubusercontent.com/eligrey/FileSaver.js/2.0.0/src/FileSaver.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://cdn.datatables.net/v/bs4/dt-1.10.18/r-2.2.2/datatables.min.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://cdn.datatables.net/v/bs4/dt-1.10.18/r-2.2.2/sl-1.3.0/datatables.min.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="html"> <span class="nt" style="color: #000080;"><script></span><span class="p">{{</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://cdnjs.cloudflare.com/ajax/libs/jquery-scrollTo/2.1.2/jquery.scrollTo.min.js</span><span class="dl">"</span><span class="o" style="font-weight: 600;">|</span><span class="nx">get_resource_as_string</span> <span class="p">}}</span><span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="html"> <span class="c" style="color: #998; font-style: italic;"><!-- Icons --></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">@@ -520,11 +628,7 @@</td>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="html"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="html"> <span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="html"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="html"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">view</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nx">vega</span><span class="p">.</span><span class="nx">View</span><span class="p">(</span><span class="nx">vega</span><span class="p">.</span><span class="nx">parse</span><span class="p">(</span><span class="nx">rulegraph_spec</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="html"> <span class="p">.</span><span class="nx">renderer</span><span class="p">(</span><span class="dl">"</span><span class="s2" style="color: #d14;">canvas</span><span class="dl">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="html"> <span class="p">.</span><span class="nx">initialize</span><span class="p">(</span><span class="dl">"</span><span class="s2" style="color: #d14;">#rulegraph</span><span class="dl">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="html"> <span class="p">.</span><span class="nx">hover</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="html"> <span class="p">.</span><span class="nx">run</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="html"> <span class="nx">vegaEmbed</span><span class="p">(</span><span class="dl">"</span><span class="s2" style="color: #d14;">#rulegraph</span><span class="dl">"</span><span class="p">,</span> <span class="nx">rulegraph_spec</span><span class="p">);</span></span>
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528
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632
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="html"></span>
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529
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="html"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">runtimes_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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530
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="html"> <span class="dl">"</span><span class="s2" style="color: #d14;">$schema</span><span class="dl">"</span><span class="p">:</span> <span class="dl">"</span><span class="s2" style="color: #d14;">https://vega.github.io/schema/vega-lite/v2.json</span><span class="dl">"</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="709" style="width: 35px; color: rgba(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">@@ -605,7 +709,7 @@</td>
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709
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="html"> <span class="p">});</span></span>
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606
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710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="html"> <span class="nx">$</span><span class="p">(</span><span class="dl">'</span><span class="s1" style="color: #d14;">.results-table</span><span class="dl">'</span><span class="p">).</span><span class="nx">DataTable</span><span class="p">();</span></span>
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608
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="html"> <span class="nx">$</span><span class="p">(</span><span class="dl">'</span><span class="s1" style="color: #d14;">#rules-table</span><span class="dl">'</span><span class="p">).</span><span class="nx">DataTable</span><span class="p">({</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="html"> <span class="kd" style="font-weight: 600;"><span class="idiff left">var</span></span><span class="idiff"> </span><span class="nx"><span class="idiff">rule_table</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="nx">$</span><span class="p">(</span><span class="dl">'</span><span class="s1" style="color: #d14;">#rules-table</span><span class="dl">'</span><span class="p">).</span><span class="nx">DataTable</span><span class="p">({</span></span>
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609
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713
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="html"> <span class="na" style="color: #008080;">paging</span><span class="p">:</span> <span class="kc" style="font-weight: 600;">false</span></span>
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610
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714
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="html"> <span class="p">});</span></span>
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715
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="html"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="726" style="width: 35px; color: rgba(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">@@ -622,6 +726,25 @@</td>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="html"> <span class="p">{</span><span class="o" style="font-weight: 600;">%</span> <span class="nx">endfor</span> <span class="o" style="font-weight: 600;">%</span><span class="p">}</span></span>
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727
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="html"> <span class="p">{</span><span class="o" style="font-weight: 600;">%</span> <span class="nx">endfor</span> <span class="o" style="font-weight: 600;">%</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="html"> <span class="c1" style="color: #998; font-style: italic;">// jump to row upon clicking rule</span></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="html"> <span class="nx">$</span><span class="p">(</span><span class="dl">"</span><span class="s2" style="color: #d14;">a.rule</span><span class="dl">"</span><span class="p">).</span><span class="nx">click</span><span class="p">(</span><span class="kd" style="font-weight: 600;">function</span><span class="p">()</span> <span class="p">{</span></span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="html"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">rule</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">$</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="p">).</span><span class="nx">html</span><span class="p">();</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="html"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">rule_table</span><span class="p">.</span><span class="nx">row</span><span class="p">(</span><span class="kd" style="font-weight: 600;">function</span> <span class="p">(</span> <span class="nx">idx</span><span class="p">,</span> <span class="nx">data</span><span class="p">,</span> <span class="nx">node</span> <span class="p">)</span> <span class="p">{</span></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="html"> <span class="k" style="font-weight: 600;">return</span> <span class="nx">data</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="nx">rule</span><span class="p">;</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="html"> <span class="p">});</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="html"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nx">row</span><span class="p">.</span><span class="nx">length</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>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="html"> <span class="nx">rule_table</span><span class="p">.</span><span class="nx">rows</span><span class="p">().</span><span class="nx">deselect</span><span class="p">();</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="html"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">node</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">row</span><span class="p">.</span><span class="nx">select</span><span class="p">().</span><span class="nx">draw</span><span class="p">().</span><span class="nx">node</span><span class="p">();</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="html"> <span class="nx">$</span><span class="p">(</span><span class="dl">"</span><span class="s2" style="color: #d14;">body</span><span class="dl">"</span><span class="p">).</span><span class="nx">scrollTo</span><span class="p">(</span><span class="nx">node</span><span class="p">);</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="html"> <span class="p">}</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="html"> <span class="p">});</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="html"></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="html"> <span class="nx">$</span><span class="p">.</span><span class="nx">extend</span><span class="p">(</span><span class="nx">$</span><span class="p">.</span><span class="nx">scrollTo</span><span class="p">.</span><span class="nx">defaults</span><span class="p">,</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="html"> <span class="na" style="color: #008080;">axis</span><span class="p">:</span> <span class="dl">'</span><span class="s1" style="color: #d14;">y</span><span class="dl">'</span><span class="p">,</span></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="html"> <span class="na" style="color: #008080;">duration</span><span class="p">:</span> <span class="mi" style="color: #099;">800</span><span class="p">,</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="html"> <span class="na" style="color: #008080;">offset</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">90</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="html"> <span class="p">});</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="html"></span>
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748
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="html"> <span class="nx">$</span><span class="p">(</span><span class="nb" style="color: #0086b3;">document</span><span class="p">).</span><span class="nx">ready</span><span class="p">(</span><span class="kd" style="font-weight: 600;">function</span><span class="p">()</span> <span class="p">{</span></span>
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626
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749
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="html"> <span class="c1" style="color: #998; font-style: italic;">// Hide loading screen when document is ready.</span></span>
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627
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750
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="html"> <span class="nx">setTimeout</span><span class="p">(</span><span class="kd" style="font-weight: 600;">function</span><span class="p">(){</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#55752111e76e9d786fdb84c4e7fd9f6de5c67a24"><strong>snakemake/rules.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" style="width: 35px; color: rgba(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="68" style="width: 35px; color: rgba(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">@@ -68,6 +68,7 @@ class Rule:</td>
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68
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68
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<pre style="margin: 0;"> <span id="LC68" 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;">is_branched</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" 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;">is_checkpoint</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" 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;">restart_times</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" 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;">basedir</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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71
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</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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72
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">other</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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73
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<pre style="margin: 0;"> <span id="LC74" 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;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">other</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="108" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,6 +109,7 @@ class Rule:</td>
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<pre style="margin: 0;"> <span id="LC109" 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;">is_branched</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="LC110" 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;">is_checkpoint</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_checkpoint</span></span>
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<pre style="margin: 0;"> <span id="LC111" 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;">restart_times</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restart_times</span></span>
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<pre style="margin: 0;">+<span id="LC112" 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;">basedir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basedir</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dynamic_branch</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">wildcards</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">input</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_io</span><span class="p">(</span><span class="n" style="color: #333;">rule</span><span class="p">):</span></span>
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<li id="66a73d9dd46eb8e71f0039a18d36dbd78aea7977">
<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#66a73d9dd46eb8e71f0039a18d36dbd78aea7977"><strong>snakemake/script.py</strong></a>
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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">@@ -227,13 +227,8 @@ class Snakemake:</td>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lookup</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 class="n" style="color: #333;">append</span><span class="p">)]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</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;">log</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">script</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">basedir</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">input</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">wildcards</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="p">,</span> <span class="n" style="color: #333;">resources</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">rulename</span><span class="p">,</span> <span class="n" style="color: #333;">conda_env</span><span class="p">,</span> <span class="n" style="color: #333;">singularity_img</span><span class="p">,</span> <span class="n" style="color: #333;">singularity_args</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">bench_record</span><span class="p">,</span> <span class="n" style="color: #333;">jobid</span><span class="p">,</span> <span class="n" style="color: #333;">bench_iteration</span><span class="p">,</span> <span class="n" style="color: #333;">shadow_dir</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"><span class="s" style="color: #d14;"> Load a script from the given basedir + path and execute it.</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"><span class="s" style="color: #d14;"> Supports Python 3 and R.</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_source</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">basedir</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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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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237
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232
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<pre style="margin: 0;"> <span id="LC232" 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;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"http"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"git+file"</span><span class="p">):</span></span>
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238
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"file://"</span><span class="p">):</span></span>
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239
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="244" style="width: 35px; color: rgba(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="239" style="width: 35px; color: rgba(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">@@ -244,225 +239,245 @@ def script(path, basedir, input, output, params, wildcards, threads, resources,</td>
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244
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"file://"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">path</span></span>
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245
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">path</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;">path</span><span class="p">,</span> <span class="n" style="color: #333;">stepout</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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246
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"file://"</span><span class="p">):</span></span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">sourceurl</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"file:"</span><span class="o" style="font-weight: 600;"><span class="idiff left right">+</span></span><span class="n" style="color: #333;">pathname2url</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:])</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">sourceurl</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"file:"</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">pathname2url</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:])</span></span>
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248
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243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"git+file"</span><span class="p">):</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">git_content</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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249
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">root_path</span><span class="p">,</span> <span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split_git_path</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="nb" style="color: #0086b3;">dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".snakemake/wrappers"</span></span>
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251
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<pre style="margin: 0;">-<span id="LC251" 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;">makedirs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dir</span><span class="p">,</span> <span class="n" style="color: #333;">exist_ok</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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252
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">new_path</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="nb" style="color: #0086b3;">dir</span><span class="p">,</span> <span class="n" style="color: #333;">version</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="s" style="color: #d14;">"-"</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;">file_path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</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="LC253" 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;">new_path</span><span class="p">,</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;">wrapper</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">wrapper</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;">git_content</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">sourceurl</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"file:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">new_path</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">path</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;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"@"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">path</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;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"@"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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257
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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258
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">sourceurl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span></span>
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<td class="diff-line-num new new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> </span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".py"</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"python"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".R"</span><span class="p">):</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"r"</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".Rmd"</span><span class="p">):</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"rmarkdown"</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".jl"</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"julia"</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> </span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">source</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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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">urlopen</span><span class="p">(</span><span class="n" style="color: #333;">sourceurl</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">source</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(),</span> <span class="n" style="color: #333;">language</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">language</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">script</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">basedir</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">input</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">wildcards</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="p">,</span> <span class="n" style="color: #333;">resources</span><span class="p">,</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">rulename</span><span class="p">,</span> <span class="n" style="color: #333;">conda_env</span><span class="p">,</span> <span class="n" style="color: #333;">singularity_img</span><span class="p">,</span> <span class="n" style="color: #333;">singularity_args</span><span class="p">,</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">bench_record</span><span class="p">,</span> <span class="n" style="color: #333;">jobid</span><span class="p">,</span> <span class="n" style="color: #333;">bench_iteration</span><span class="p">,</span> <span class="n" style="color: #333;">shadow_dir</span><span class="p">):</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"><span class="s" style="color: #d14;"> Load a script from the given basedir + path and execute it.</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"><span class="s" style="color: #d14;"> Supports Python 3 and R.</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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259
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"></span>
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260
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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261
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">urlopen</span><span class="p">(</span><span class="n" style="color: #333;">sourceurl</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">source</span><span class="p">:</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".py"</span><span class="p">):</span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">wrapper_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"file://"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">path</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">snakemake</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Snakemake</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">wildcards</span><span class="p">,</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">threads</span><span class="p">,</span> <span class="n" style="color: #333;">resources</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">rulename</span><span class="p">,</span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">bench_iteration</span><span class="p">,</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" 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;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">wrapper_path</span><span class="p">))</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">snakemake</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pickle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dumps</span><span class="p">(</span><span class="n" style="color: #333;">snakemake</span><span class="p">)</span></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Obtain search path for current snakemake module.</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The module is needed for unpickling in the script.</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># We append it at the end (as a fallback).</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">searchpath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SNAKEMAKE_SEARCHPATH</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">singularity_img</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="LC275" class="line" lang="python"> <span class="n" style="color: #333;">searchpath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">singularity</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SNAKEMAKE_MOUNTPOINT</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">searchpath</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="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">searchpath</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># For local scripts, add their location to the path in case they use path-based imports</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"file://"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">searchpath</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="nb" style="color: #0086b3;">format</span><span class="p">(</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:]))</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">preamble</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textwrap</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;"> ######## Snakemake header ########</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"><span class="s" style="color: #d14;"> import sys; sys.path.extend([{searchpath}]); import pickle; snakemake = pickle.loads({snakemake}); from snakemake.logging import logger; logger.printshellcmds = {printshellcmds}; __real_file__ = __file__; __file__ = {file_override};</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"><span class="s" style="color: #d14;"> ######## Original script #########</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"><span class="s" style="color: #d14;"> """</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">searchpath</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">escape_backslash</span><span class="p">(</span><span class="n" style="color: #333;">searchpath</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">snakemake</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">snakemake</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">printshellcmds</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">printshellcmds</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">file_override</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">(</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;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">wrapper_path</span><span class="p">)))</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".R"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".Rmd"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">preamble</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textwrap</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"><span class="s" style="color: #d14;"> ######## Snakemake header ########</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"><span class="s" style="color: #d14;"> library(methods)</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"><span class="s" style="color: #d14;"> Snakemake <- setClass(</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"><span class="s" style="color: #d14;"> "Snakemake",</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"><span class="s" style="color: #d14;"> slots = c(</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"><span class="s" style="color: #d14;"> input = "list",</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"><span class="s" style="color: #d14;"> output = "list",</span></span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"><span class="s" style="color: #d14;"> params = "list",</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"><span class="s" style="color: #d14;"> wildcards = "list",</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"><span class="s" style="color: #d14;"> threads = "numeric",</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"><span class="s" style="color: #d14;"> log = "list",</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"><span class="s" style="color: #d14;"> resources = "list",</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"><span class="s" style="color: #d14;"> config = "list",</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"><span class="s" style="color: #d14;"> rule = "character",</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"><span class="s" style="color: #d14;"> bench_iteration = "numeric",</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"><span class="s" style="color: #d14;"> scriptdir = "character",</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"><span class="s" style="color: #d14;"> source = "function"</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_source</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">basedir</span><span class="p">)</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"python"</span><span class="p">:</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">wrapper_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"file://"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">path</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">snakemake</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Snakemake</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">wildcards</span><span class="p">,</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">threads</span><span class="p">,</span> <span class="n" style="color: #333;">resources</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">rulename</span><span class="p">,</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">bench_iteration</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC283" 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;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">wrapper_path</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">snakemake</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pickle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dumps</span><span class="p">(</span><span class="n" style="color: #333;">snakemake</span><span class="p">)</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Obtain search path for current snakemake module.</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The module is needed for unpickling in the script.</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># We append it at the end (as a fallback).</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">searchpath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SNAKEMAKE_SEARCHPATH</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">singularity_img</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="LC290" class="line" lang="python"> <span class="n" style="color: #333;">searchpath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">singularity</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SNAKEMAKE_MOUNTPOINT</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">searchpath</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="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">searchpath</span><span class="p">)</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># For local scripts, add their location to the path in case they use path-based imports</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"file://"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">searchpath</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="nb" style="color: #0086b3;">format</span><span class="p">(</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:]))</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">preamble</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textwrap</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"><span class="s" style="color: #d14;"> ######## Snakemake header ########</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"><span class="s" style="color: #d14;"> import sys; sys.path.extend([{searchpath}]); import pickle; snakemake = pickle.loads({snakemake}); from snakemake.logging import logger; logger.printshellcmds = {printshellcmds}; __real_file__ = __file__; __file__ = {file_override};</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"><span class="s" style="color: #d14;"> ######## Original script #########</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"><span class="s" style="color: #d14;"> """</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">searchpath</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">escape_backslash</span><span class="p">(</span><span class="n" style="color: #333;">searchpath</span><span class="p">),</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">snakemake</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">snakemake</span><span class="p">,</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">printshellcmds</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">printshellcmds</span><span class="p">,</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">file_override</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">(</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;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">wrapper_path</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"r"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"rmarkdown"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">preamble</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textwrap</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">"""</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"><span class="s" style="color: #d14;"> ######## Snakemake header ########</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"><span class="s" style="color: #d14;"> library(methods)</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"><span class="s" style="color: #d14;"> Snakemake <- setClass(</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"><span class="s" style="color: #d14;"> "Snakemake",</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"><span class="s" style="color: #d14;"> slots = c(</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"><span class="s" style="color: #d14;"> input = "list",</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"><span class="s" style="color: #d14;"> output = "list",</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"><span class="s" style="color: #d14;"> params = "list",</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"><span class="s" style="color: #d14;"> wildcards = "list",</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"><span class="s" style="color: #d14;"> threads = "numeric",</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"><span class="s" style="color: #d14;"> log = "list",</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"><span class="s" style="color: #d14;"> resources = "list",</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"><span class="s" style="color: #d14;"> config = "list",</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"><span class="s" style="color: #d14;"> rule = "character",</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"><span class="s" style="color: #d14;"> bench_iteration = "numeric",</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"><span class="s" style="color: #d14;"> scriptdir = "character",</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"><span class="s" style="color: #d14;"> source = "function"</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"><span class="s" style="color: #d14;"> snakemake <- Snakemake(</span></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"><span class="s" style="color: #d14;"> input = {},</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python"><span class="s" style="color: #d14;"> output = {},</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"><span class="s" style="color: #d14;"> params = {},</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"><span class="s" style="color: #d14;"> wildcards = {},</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"><span class="s" style="color: #d14;"> threads = {},</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"><span class="s" style="color: #d14;"> log = {},</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"><span class="s" style="color: #d14;"> resources = {},</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"><span class="s" style="color: #d14;"> config = {},</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"><span class="s" style="color: #d14;"> rule = {},</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"><span class="s" style="color: #d14;"> bench_iteration = {},</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"><span class="s" style="color: #d14;"> scriptdir = {},</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"><span class="s" style="color: #d14;"> source = function(...){{</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"><span class="s" style="color: #d14;"> wd <- getwd()</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"><span class="s" style="color: #d14;"> setwd(snakemake@scriptdir)</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"><span class="s" style="color: #d14;"> source(...)</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="python"><span class="s" style="color: #d14;"> setwd(wd)</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"><span class="s" style="color: #d14;"> }}</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"><span class="s" style="color: #d14;"> snakemake <- Snakemake(</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"><span class="s" style="color: #d14;"> input = {},</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"><span class="s" style="color: #d14;"> output = {},</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"><span class="s" style="color: #d14;"> params = {},</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"><span class="s" style="color: #d14;"> wildcards = {},</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"><span class="s" style="color: #d14;"> threads = {},</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"><span class="s" style="color: #d14;"> log = {},</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"><span class="s" style="color: #d14;"> resources = {},</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"><span class="s" style="color: #d14;"> config = {},</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"><span class="s" style="color: #d14;"> rule = {},</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"><span class="s" style="color: #d14;"> bench_iteration = {},</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"><span class="s" style="color: #d14;"> scriptdir = {},</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"><span class="s" style="color: #d14;"> source = function(...){{</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"><span class="s" style="color: #d14;"> wd <- getwd()</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"><span class="s" style="color: #d14;"> setwd(snakemake@scriptdir)</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"><span class="s" style="color: #d14;"> source(...)</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"><span class="s" style="color: #d14;"> setwd(wd)</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"><span class="s" style="color: #d14;"> }}</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"><span class="s" style="color: #d14;"> ######## Original script #########</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"><span class="s" style="color: #d14;"> """</span><span class="p">)</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;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">),</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">),</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">),</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">wildcards</span><span class="p">),</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">threads</span><span class="p">,</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">log</span><span class="p">),</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">({</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">value</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</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;">resources</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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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"_cores"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"_nodes"</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"> <span class="p">}),</span> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_dict</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">),</span> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_value</span><span class="p">(</span><span class="n" style="color: #333;">rulename</span><span class="p">),</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_numeric</span><span class="p">(</span><span class="n" style="color: #333;">bench_iteration</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_value</span><span class="p">(</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"file://"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)))</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"julia"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">preamble</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textwrap</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">"""</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"><span class="s" style="color: #d14;"> ######## Snakemake header ########</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"><span class="s" style="color: #d14;"> struct Snakemake</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"><span class="s" style="color: #d14;"> input::Dict</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"><span class="s" style="color: #d14;"> output::Dict</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"><span class="s" style="color: #d14;"> params::Dict</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"><span class="s" style="color: #d14;"> wildcards::Dict</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"><span class="s" style="color: #d14;"> threads::Int64</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"><span class="s" style="color: #d14;"> log::Dict</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"><span class="s" style="color: #d14;"> resources::Dict</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"><span class="s" style="color: #d14;"> config::Dict</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"><span class="s" style="color: #d14;"> rule::String</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"><span class="s" style="color: #d14;"> bench_iteration</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"><span class="s" style="color: #d14;"> scriptdir::String</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"><span class="s" style="color: #d14;"> #source::Any</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"><span class="s" style="color: #d14;"> end</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"><span class="s" style="color: #d14;"> snakemake = Snakemake(</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #input::Dict</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #output::Dict</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #params::Dict</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #wildcards::Dict</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #threads::Int64</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #log::Dict</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #resources::Dict</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #config::Dict</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #rule::String</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #bench_iteration::Int64</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #scriptdir::String</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"><span class="s" style="color: #d14;"> #, #source::Any</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"><span class="s" style="color: #d14;"> ######## Original script #########</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"><span class="s" style="color: #d14;"> """</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">),</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">),</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">),</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">wildcards</span><span class="p">),</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_value</span><span class="p">(</span><span class="n" style="color: #333;">threads</span><span class="p">),</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">log</span><span class="p">),</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">({</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">value</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</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;">resources</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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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"_cores"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"_nodes"</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="p">}),</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_dict</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_value</span><span class="p">(</span><span class="n" style="color: #333;">rulename</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_value</span><span class="p">(</span><span class="n" style="color: #333;">bench_iteration</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_value</span><span class="p">(</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"file://"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC409" 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="LC410" 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>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="s" style="color: #d14;">"Unsupported script: Expecting either Python (.py), R (.R), RMarkdown (.Rmd) or Julia (.jl) script."</span><span class="p">)</span></span>
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python"><span class="s" style="color: #d14;"> ######## Original script #########</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python"><span class="s" style="color: #d14;"> """</span><span class="p">)</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;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">wildcards</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">threads</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">log</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">({</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">value</span></span>
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339
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</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;">resources</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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340
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"_cores"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"_nodes"</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"> <span class="p">}),</span> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_dict</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">),</span> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_value</span><span class="p">(</span><span class="n" style="color: #333;">rulename</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_numeric</span><span class="p">(</span><span class="n" style="color: #333;">bench_iteration</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">REncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_value</span><span class="p">(</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"file://"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)))</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".jl"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">preamble</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textwrap</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"><span class="s" style="color: #d14;"> ######## Snakemake header ########</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="python"><span class="s" style="color: #d14;"> struct Snakemake</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python"><span class="s" style="color: #d14;"> input::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"><span class="s" style="color: #d14;"> output::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"><span class="s" style="color: #d14;"> params::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python"><span class="s" style="color: #d14;"> wildcards::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"><span class="s" style="color: #d14;"> threads::Int64</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python"><span class="s" style="color: #d14;"> log::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python"><span class="s" style="color: #d14;"> resources::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python"><span class="s" style="color: #d14;"> config::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python"><span class="s" style="color: #d14;"> rule::String</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="python"><span class="s" style="color: #d14;"> bench_iteration</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python"><span class="s" style="color: #d14;"> scriptdir::String</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"><span class="s" style="color: #d14;"> #source::Any</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"><span class="s" style="color: #d14;"> end</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python"><span class="s" style="color: #d14;"> snakemake = Snakemake(</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #input::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #output::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #params::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #wildcards::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #threads::Int64</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #log::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #resources::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #config::Dict</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #rule::String</span></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #bench_iteration::Int64</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #scriptdir::String</span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"><span class="s" style="color: #d14;"> #, #source::Any</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="python"><span class="s" style="color: #d14;"> ######## Original script #########</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"><span class="s" style="color: #d14;"> """</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">wildcards</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_value</span><span class="p">(</span><span class="n" style="color: #333;">threads</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">(</span><span class="n" style="color: #333;">log</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_namedlist</span><span class="p">({</span></span>
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">value</span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</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;">resources</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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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"_cores"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"_nodes"</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"> <span class="p">}),</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_dict</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_value</span><span class="p">(</span><span class="n" style="color: #333;">rulename</span><span class="p">),</span></span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_value</span><span class="p">(</span><span class="n" style="color: #333;">bench_iteration</span><span class="p">),</span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">JuliaEncoder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_value</span><span class="p">(</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"file://"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python"> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python"> <span class="p">)</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"> <span class="nb" style="color: #0086b3;">dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".snakemake/scripts"</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" 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;">makedirs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dir</span><span class="p">,</span> <span class="n" style="color: #333;">exist_ok</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</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>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"> <span class="n" style="color: #333;">suffix</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;">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;">basename</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">),</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">dir</span><span class="p">,</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"> <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 class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" 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;">language</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"rmarkdown"</span><span class="p">:</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">f</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;">preamble</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">f</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;">source</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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395
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<pre style="margin: 0;">-<span id="LC395" 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>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="python"> <span class="s" style="color: #d14;">"Unsupported script: Expecting either Python (.py), R (.R), RMarkdown (.Rmd) or Julia (.jl) script."</span><span class="p">)</span></span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"> <span class="nb" style="color: #0086b3;">dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".snakemake/scripts"</span></span>
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<pre style="margin: 0;">-<span id="LC399" 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;">makedirs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dir</span><span class="p">,</span> <span class="n" style="color: #333;">exist_ok</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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400
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</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>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="python"> <span class="n" style="color: #333;">suffix</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;">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;">basename</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">),</span></span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="python"> <span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">dir</span><span class="p">,</span></span>
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404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python"> <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 class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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405
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<pre style="margin: 0;">-<span id="LC405" 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;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".Rmd"</span><span class="p">):</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">f</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;">preamble</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode</span><span class="p">())</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">f</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;">source</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">())</span></span>
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408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Insert Snakemake object after the RMarkdown header</span></span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">()</span></span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">islice</span><span class="p">(</span><span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">finditer</span><span class="p">(</span><span class="s" style="color: #d14;">r"---\n"</span><span class="p">,</span> <span class="n" style="color: #333;">code</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">3</span></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="n" style="color: #333;">code</span><span class="p">[:</span><span class="n" style="color: #333;">pos</span><span class="p">]))</span></span>
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413
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">preamble</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textwrap</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">"""</span></span>
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414
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="python"><span class="s" style="color: #d14;"> ```{r, echo=FALSE, message=FALSE, warning=FALSE}</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span></span>
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416
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"><span class="s" style="color: #d14;"> ```</span></span>
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417
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python"><span class="s" style="color: #d14;"> """</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">preamble</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">f</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;">preamble</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="n" style="color: #333;">code</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">:]))</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".py"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">py_exec</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;">executable</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">conda_env</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="LC424" class="line" lang="python"> <span class="n" style="color: #333;">py</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;">conda_env</span><span class="p">,</span> <span class="s" style="color: #d14;">"bin"</span><span class="p">,</span> <span class="s" style="color: #d14;">"python"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC425" 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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">py</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">out</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;">check_output</span><span class="p">([</span><span class="n" style="color: #333;">py</span><span class="p">,</span> <span class="s" style="color: #d14;">"--version"</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;">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;">STDOUT</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">universal_newlines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="python"> <span class="n" style="color: #333;">ver</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">PY_VER_RE</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="s" style="color: #d14;">"ver_min"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</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="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ver</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">MIN_PY_VERSION</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Python version is new enough, make use of environment</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># to execute script</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">py_exec</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"python"</span></span>
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<pre style="margin: 0;">-<span id="LC434" 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="LC435" 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;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Conda environment defines Python "</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="python"> <span class="s" style="color: #d14;">"version < {0}.{1}. Using Python of the "</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="python"> <span class="s" style="color: #d14;">"master process to execute "</span></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="python"> <span class="s" style="color: #d14;">"script. Note that this cannot be avoided, "</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="python"> <span class="s" style="color: #d14;">"because the script uses data structures from "</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="python"> <span class="s" style="color: #d14;">"Snakemake which are Python >={0}.{1} "</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="python"> <span class="s" style="color: #d14;">"only."</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">MIN_PY_VERSION</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">singularity_img</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="LC443" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># use python from image</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">py_exec</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"python"</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># use the same Python as the running process or the one from the environment</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="python"> <span class="n" style="color: #333;">shell</span><span class="p">(</span><span class="s" style="color: #d14;">"{py_exec} {f.name:q}"</span><span class="p">,</span> <span class="n" style="color: #333;">bench_record</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bench_record</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".R"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">conda_env</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="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"R_LIBS"</span> <span class="ow" style="font-weight: 600;">in</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="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC449" 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;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"R script job uses conda environment but "</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="python"> <span class="s" style="color: #d14;">"R_LIBS environment variable is set. This "</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="python"> <span class="s" style="color: #d14;">"is likely not intended, as R_LIBS can "</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="python"> <span class="s" style="color: #d14;">"interfere with R packages deployed via "</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="python"> <span class="s" style="color: #d14;">"conda. Consider running `unset R_LIBS` or "</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="python"> <span class="s" style="color: #d14;">"remove it entirely before executing "</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="python"> <span class="s" style="color: #d14;">"Snakemake."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="python"> <span class="n" style="color: #333;">shell</span><span class="p">(</span><span class="s" style="color: #d14;">"Rscript --vanilla {f.name:q}"</span><span class="p">,</span> <span class="n" style="color: #333;">bench_record</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bench_record</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".Rmd"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC458" 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;">output</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="LC459" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span><span class="s" style="color: #d14;">"RMarkdown scripts (.Rmd) may only have a single output file."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="python"> <span class="n" style="color: #333;">out</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;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="python"> <span class="n" style="color: #333;">shell</span><span class="p">(</span><span class="s" style="color: #d14;">"Rscript --vanilla -e 'rmarkdown::render(</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">{f.name}</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">, output_file=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">{out}</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">, quiet=TRUE, knit_root_dir = </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">{workdir}</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">, params = list(rmd=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">{f.name}</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">))'"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="python"> <span class="n" style="color: #333;">bench_record</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bench_record</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="python"> <span class="n" style="color: #333;">workdir</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>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".jl"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;">shell</span><span class="p">(</span><span class="s" style="color: #d14;">"julia {f.name:q}"</span><span class="p">,</span> <span class="n" style="color: #333;">bench_record</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bench_record</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Insert Snakemake object after the RMarkdown header</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">islice</span><span class="p">(</span><span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">finditer</span><span class="p">(</span><span class="s" style="color: #d14;">r"---\n"</span><span class="p">,</span> <span class="n" style="color: #333;">code</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">3</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="n" style="color: #333;">code</span><span class="p">[:</span><span class="n" style="color: #333;">pos</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">preamble</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textwrap</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"><span class="s" style="color: #d14;"> ```{r, echo=FALSE, message=FALSE, warning=FALSE}</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"><span class="s" style="color: #d14;"> ```</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"><span class="s" style="color: #d14;"> """</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">preamble</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">f</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;">preamble</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode</span><span class="p">())</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="n" style="color: #333;">code</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">:]))</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python"></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"python"</span><span class="p">:</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"> <span class="n" style="color: #333;">py_exec</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;">executable</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">conda_env</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="LC439" class="line" lang="python"> <span class="n" style="color: #333;">py</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;">conda_env</span><span class="p">,</span> <span class="s" style="color: #d14;">"bin"</span><span class="p">,</span> <span class="s" style="color: #d14;">"python"</span><span class="p">)</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" 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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">py</span><span class="p">):</span></span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python"> <span class="n" style="color: #333;">out</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;">check_output</span><span class="p">([</span><span class="n" style="color: #333;">py</span><span class="p">,</span> <span class="s" style="color: #d14;">"--version"</span><span class="p">],</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <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;">STDOUT</span><span class="p">,</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">universal_newlines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">ver</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">PY_VER_RE</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="s" style="color: #d14;">"ver_min"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">)))</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ver</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">MIN_PY_VERSION</span><span class="p">:</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Python version is new enough, make use of environment</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># to execute script</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"> <span class="n" style="color: #333;">py_exec</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"python"</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" 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;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Conda environment defines Python "</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"> <span class="s" style="color: #d14;">"version < {0}.{1}. Using Python of the "</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="s" style="color: #d14;">"master process to execute "</span></span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="s" style="color: #d14;">"script. Note that this cannot be avoided, "</span></span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="python"> <span class="s" style="color: #d14;">"because the script uses data structures from "</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"> <span class="s" style="color: #d14;">"Snakemake which are Python >={0}.{1} "</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="python"> <span class="s" style="color: #d14;">"only."</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">MIN_PY_VERSION</span><span class="p">))</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">singularity_img</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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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># use python from image</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">py_exec</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"python"</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># use the same Python as the running process or the one from the environment</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python"> <span class="n" style="color: #333;">shell</span><span class="p">(</span><span class="s" style="color: #d14;">"{py_exec} {f.name:q}"</span><span class="p">,</span> <span class="n" style="color: #333;">bench_record</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bench_record</span><span class="p">)</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"r"</span><span class="p">:</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">conda_env</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="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"R_LIBS"</span> <span class="ow" style="font-weight: 600;">in</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="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC464" 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;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"R script job uses conda environment but "</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="python"> <span class="s" style="color: #d14;">"R_LIBS environment variable is set. This "</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="python"> <span class="s" style="color: #d14;">"is likely not intended, as R_LIBS can "</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"> <span class="s" style="color: #d14;">"interfere with R packages deployed via "</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"> <span class="s" style="color: #d14;">"conda. Consider running `unset R_LIBS` or "</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="s" style="color: #d14;">"remove it entirely before executing "</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"> <span class="s" style="color: #d14;">"Snakemake."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"> <span class="n" style="color: #333;">shell</span><span class="p">(</span><span class="s" style="color: #d14;">"Rscript --vanilla {f.name:q}"</span><span class="p">,</span> <span class="n" style="color: #333;">bench_record</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bench_record</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"rmarkdown"</span><span class="p">:</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" 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;">output</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="LC474" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span><span class="s" style="color: #d14;">"RMarkdown scripts (.Rmd) may only have a single output file."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"> <span class="n" style="color: #333;">out</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;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">[</span><span class="mi" style="color: #099;">0</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;">shell</span><span class="p">(</span><span class="s" style="color: #d14;">"Rscript --vanilla -e 'rmarkdown::render(</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">{f.name}</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">, output_file=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">{out}</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">, quiet=TRUE, knit_root_dir = </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">{workdir}</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">, params = list(rmd=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">{f.name}</span><span class="se" style="color: #d14;">\"</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;">bench_record</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bench_record</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;">workdir</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>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"julia"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="n" style="color: #333;">shell</span><span class="p">(</span><span class="s" style="color: #d14;">"julia {f.name:q}"</span><span class="p">,</span> <span class="n" style="color: #333;">bench_record</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bench_record</span><span class="p">)</span></span>
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="python"></span>
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467
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482
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">URLError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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483
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#cb9e107597e441fb1c0d61663359d9cf1dbfe04d"><strong>snakemake/workflow.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="896" style="width: 35px; color: rgba(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="896" style="width: 35px; color: rgba(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">@@ -896,6 +896,7 @@ class Workflow:</td>
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896
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896
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<pre style="margin: 0;"> <span id="LC896" class="line" lang="python"> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wrapper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ruleinfo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wrapper</span></span>
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897
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897
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<pre style="margin: 0;"> <span id="LC897" class="line" lang="python"> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cwl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ruleinfo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cwl</span></span>
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898
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898
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<pre style="margin: 0;"> <span id="LC898" class="line" lang="python"> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restart_times</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;">restart_times</span></span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="python"> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basedir</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;">current_basedir</span></span>
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899
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="python"></span>
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900
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="python"> <span class="n" style="color: #333;">ruleinfo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">func</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</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="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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901
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902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">globals</span><span class="p">[</span><span class="n" style="color: #333;">ruleinfo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">func</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ruleinfo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">func</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/compare/703c50a3f500e83b1253f79237bd607ee426127c...dbc52a27594fb0ae7f1cea2c7c37b62e2c2f54ce#d1deee71de70305809d43086b13f7eb407aff6f2"><strong>test-environment.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -19,6 +19,7 @@ dependencies:</td>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">appdirs</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pytools</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docutils</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pygments</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pandoc <2.0</span> <span class="c1" style="color: #998; font-style: italic;"># pandoc has changed the CLI API so that it is no longer compatible with the version of r-markdown below</span></span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">xorg-libxrender</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">xorg-libxext</span></span>
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