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GitLab

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<h3>

Rebecca N. Palmer pushed to branch upstream

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/ede461d574af316927b0b43b0637e75795ba0d17">ede461d5</a></strong>

<div>

<span>by Rebecca N. Palmer</span>

<i>at 2020-08-16T13:19:27+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.22.1</pre>

</li>

</ul>

<h4>27 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#c778226b6c4c0fb51cf7942c8ee1f3d9fc1249d0">

.github/workflows/main.yml

</a>

</li>

<li class="file-stats">

<a href="#45267e3a9556cafa9cb7b61dab7a3b6659e73aad">

CHANGELOG.rst

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<li class="file-stats">

<a href="#0834ae016f8fea5cff771880c0be1d55299732ff">

<span class="new-file">

+

CODE_OF_CONDUCT.md

</span>

</a>

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<li class="file-stats">

<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">

Dockerfile

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<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

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<li class="file-stats">

<a href="#9983a3122073938d03b572d4b73df73fe03efe7d">

docs/_static/theme.css

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<li class="file-stats">

<a href="#254a2da7a740675e537439eb88e32083b9ea4771">

docs/conf.py

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<li class="file-stats">

<a href="#7e143b2e3a88fc7b437114c03b2302f5afa981ec">

docs/executing/cloud.rst

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<li class="file-stats">

<a href="#18336bcf377dc39d1fe1a9f38b710df68bb084fb">

<span class="new-file">

+

docs/executor_tutorial/azure_aks.rst

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<li class="file-stats">

<a href="#a51db43db8671eca05cb09411a68924732699541">

docs/executor_tutorial/google_lifesciences.rst

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<li class="file-stats">

<a href="#cd3fd8615ae98556916b352d1dff137ff81c4027">

docs/executor_tutorial/tutorial.rst

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<a href="#d0153cac95479af9bfb99b746b633bc8255bb53a">

docs/index.rst

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<a href="#4d96bc0560e0c9e4668ccb39b500cece62a72820">

docs/project_info/authors.rst

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<li class="file-stats">

<a href="#945ec74fc1c17902d98bca84b7a1f0dfd755c01b">

docs/snakefiles/deployment.rst

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<a href="#678d7e50121966ef613372bf85b3e7f144e00ef1">

docs/snakefiles/remote_files.rst

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<li class="file-stats">

<a href="#f2ad3e3ae7fe1cf3ff9f5d75e080faf74d1d8980">

docs/snakefiles/reporting.rst

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

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<li class="file-stats">

<a href="#d366205d7cd679ff6d4a61f70728e92537101763">

snakemake/__init__.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="#7610d24f21cc1508e60687b4a0c7e940a75ca358">

snakemake/executors/__init__.py

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<li class="file-stats">

<a href="#09eebb28d24925c2b41cf2365dd083ada597795e">

snakemake/executors/google_lifesciences.py

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<li class="file-stats">

<a href="#93a82c4f9627ca07fc8ef809981ab851baae987e">

snakemake/remote/AzureStorage.py

→

snakemake/remote/AzBlob.py

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<li class="file-stats">

<a href="#7e910b8868374c8ee0002ac6d034da0012544b27">

snakemake/remote/GS.py

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<li class="file-stats">

<a href="#1ffa1b3765afe0782e1886aa5b41999ae4d03543">

snakemake/resources.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="#18051d6fa83e6daf8ee96c3f5093a8d27095f4fa">

tests/common.py

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<li class="file-stats">

<a href="#d67f606b4bee14c69feeb3f0aa59bb04fdd7bd36">

tests/test_remote_azure/Snakefile

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<h4>Changes:</h4>

<li id="c778226b6c4c0fb51cf7942c8ee1f3d9fc1249d0">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#c778226b6c4c0fb51cf7942c8ee1f3d9fc1249d0"><strong>.github/workflows/main.yml</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -94,7 +94,7 @@ jobs:</td>

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

94

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

94

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="yaml">          <span class="s" style="color: #d14;">pytest -s -v -x tests/test_kubernetes.py</span></span>

</pre>

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

95

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

95

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="yaml"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Test AWS execution</span></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="yaml">        <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">env.AWS_AVAILABLE && <span class="idiff left right">success(</span>)</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="yaml">        <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">env.AWS_AVAILABLE && <span class="idiff left right">(success() || failure()</span>)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="yaml">        <span class="na" style="color: #008080;">env</span><span class="pi">:</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(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="LC99" class="line" lang="yaml">          <span class="na" style="color: #008080;">CI</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="yaml">        <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,7 +105,7 @@ jobs:</td>

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

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="yaml">          <span class="s" style="color: #d14;">pytest -v -x tests/test_tibanna.py</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="yaml"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(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="LC107" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Test Google Life Sciences Executor</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="yaml">        <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">env.GCP_AVAILABLE</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

108

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="yaml">        <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">env.GCP_AVAILABLE<span class="idiff left right"> && (success() || failure())</span></span></span>

</pre>

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

109

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109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="yaml">        <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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110

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="yaml">          <span class="s" style="color: #d14;"># activate conda env</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<td class="diff-line-num new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="yaml">          <span class="s" style="color: #d14;">export PATH="/usr/share/miniconda/bin:$PATH"</span></span>

</pre>

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</table>

<br>

</li>

<li id="45267e3a9556cafa9cb7b61dab7a3b6659e73aad">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#45267e3a9556cafa9cb7b61dab7a3b6659e73aad"><strong>CHANGELOG.rst</strong></a>

<hr>

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

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

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[5.22.1] - 2020-08-14</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">=====================</span>

</pre>

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

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

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Changed</span>

</pre>

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

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

4

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

</pre>

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

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

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">- Fixed a missing dependency for google storage in cloud execution.</span>

</pre>

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

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6

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

</pre>

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

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

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[5.22.0] - 2020-08-13</span>

</pre>

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

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

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">=====================</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Added</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">-----</span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">- Added short option ``-T`` for CLI parameter ``--restart-times`` (@mbhall88).</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">-------</span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">- Various small fixes for google storage and life sciences backends (@vsoch).</span>

</pre>

</td>

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

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

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>

</pre>

</td>

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

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

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>

</pre>

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

18

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

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">[5.21.0] - 2020-08-11</span>

</pre>

</td>

</tr>

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

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

19

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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="LC19" class="line" lang="plaintext">=====================</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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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="LC20" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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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="LC21" class="line" lang="plaintext">Changed</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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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="LC22" class="line" lang="plaintext">-------</span>

</pre>

</td>

</tr>

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

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

</td>

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

23

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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="LC23" class="line" lang="plaintext">- Added default-remote-provider support for Azure storage (@andreas-wilm).</span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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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="LC24" class="line" lang="plaintext">- Various small bug fixes and documentation improvements.</span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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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="LC25" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

</td>

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

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

</pre>

</td>

</tr>

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

1

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">[5.20.1] - 2020-07-08</span>

</pre>

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

2

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

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

<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">=====================</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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

29

</td>

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

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

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="0834ae016f8fea5cff771880c0be1d55299732ff">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#0834ae016f8fea5cff771880c0be1d55299732ff"><strong>CODE_OF_CONDUCT.md</strong></a>

<hr>

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

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

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

</td>

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"></span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<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="markdown"><span class="gh" style="color: #999;"># Contributor Covenant Code of Conduct</span></span>

</pre>

</td>

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

</td>

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

3

</td>

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

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

</td>

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

4

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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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Our Pledge</span></span>

</pre>

</td>

</tr>

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

</td>

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

5

</td>

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown">We as members, contributors, and leaders pledge to make participation in our</span>

</pre>

</td>

</tr>

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

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

</td>

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

7

</td>

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">community a harassment-free experience for everyone, regardless of age, body</span>

</pre>

</td>

</tr>

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

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

</td>

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

8

</td>

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown">size, visible or invisible disability, ethnicity, sex characteristics, gender</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">identity and expression, level of experience, education, socio-economic status,</span>

</pre>

</td>

</tr>

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

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</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">nationality, personal appearance, race, religion, or sexual identity</span>

</pre>

</td>

</tr>

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

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

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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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="LC11" class="line" lang="markdown">and orientation.</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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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="LC12" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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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="LC13" class="line" lang="markdown">We pledge to act and interact in ways that contribute to an open, welcoming,</span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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

<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">diverse, inclusive, and healthy community.</span>

</pre>

</td>

</tr>

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

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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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="LC15" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

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

16

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

<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Our Standards</span></span>

</pre>

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

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

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

<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

</td>

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

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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="LC18" class="line" lang="markdown">Examples of behavior that contributes to a positive environment for our</span>

</pre>

</td>

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

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

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

<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown">community include:</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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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="LC20" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

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

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(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="LC21" class="line" lang="markdown"><span class="p">*</span> Demonstrating empathy and kindness toward other people</span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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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="LC22" class="line" lang="markdown"><span class="p">*</span> Being respectful of differing opinions, viewpoints, and experiences</span>

</pre>

</td>

</tr>

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

</td>

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

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

<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p">*</span> Giving and gracefully accepting constructive feedback</span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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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="LC24" class="line" lang="markdown"><span class="p">*</span> Accepting responsibility and apologizing to those affected by our mistakes,</span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">  and learning from the experience</span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p">*</span> Focusing on what is best not just for us as individuals, but for the</span>

</pre>

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

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

27

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

<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown">  overall community</span>

</pre>

</td>

</tr>

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

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

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

<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

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

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

<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">Examples of unacceptable behavior include:</span>

</pre>

</td>

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

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

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

<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p">*</span> The use of sexualized language or imagery, and sexual attention or</span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">  advances of any kind</span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="p">*</span> Trolling, insulting or derogatory comments, and personal or political attacks</span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p">*</span> Public or private harassment</span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="p">*</span> Publishing others' private information, such as a physical or email</span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown">  address, without their explicit permission</span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="p">*</span> Other conduct which could reasonably be considered inappropriate in a</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Enforcement Responsibilities</span></span>

</pre>

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

</pre>

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

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown">Community leaders are responsible for clarifying and enforcing our standards of</span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown">acceptable behavior and will take appropriate and fair corrective action in</span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown">response to any behavior that they deem inappropriate, threatening, offensive,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown">or harmful.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown">Community leaders have the right and responsibility to remove, edit, or reject</span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown">comments, commits, code, wiki edits, issues, and other contributions that are</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown">not aligned to this Code of Conduct, and will communicate reasons for moderation</span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">decisions when appropriate.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Scope</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown">This Code of Conduct applies within all community spaces, and also applies when</span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown">an individual is officially representing the community in public spaces.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown">Examples of representing our community include using an official e-mail address,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown">posting via an official social media account, or acting as an appointed</span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown">representative at an online or offline event.</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Enforcement</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown">Instances of abusive, harassing, or otherwise unacceptable behavior may be</span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown">reported via email to johannes.koester@uni-due.de.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown">All complaints will be reviewed and investigated promptly and fairly.</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown">All community leaders are obligated to respect the privacy and security of the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown">reporter of any incident.</span>

</pre>

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

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Enforcement Guidelines</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown">Community leaders will follow these Community Impact Guidelines in determining</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown">the consequences for any action they deem in violation of this Code of Conduct:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 1. Correction</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Community Impact**</span>: Use of inappropriate language or other behavior deemed</span>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown">unprofessional or unwelcome in the community.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Consequence**</span>: A private, written warning from community leaders, providing</span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown">clarity around the nature of the violation and an explanation of why the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown">behavior was inappropriate. A public apology may be requested.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 2. Warning</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Community Impact**</span>: A violation through a single incident or series</span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown">of actions.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Consequence**</span>: A warning with consequences for continued behavior. No</span>

</pre>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown">interaction with the people involved, including unsolicited interaction with</span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown">those enforcing the Code of Conduct, for a specified period of time. This</span>

</pre>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown">includes avoiding interactions in community spaces as well as external channels</span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown">like social media. Violating these terms may lead to a temporary or</span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown">permanent ban.</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 3. Temporary Ban</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Community Impact**</span>: A serious violation of community standards, including</span>

</pre>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown">sustained inappropriate behavior.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Consequence**</span>: A temporary ban from any sort of interaction or public</span>

</pre>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown">communication with the community for a specified period of time. No public or</span>

</pre>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown">private interaction with the people involved, including unsolicited interaction</span>

</pre>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown">with those enforcing the Code of Conduct, is allowed during this period.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown">Violating these terms may lead to a permanent ban.</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 4. Permanent Ban</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Community Impact**</span>: Demonstrating a pattern of violation of community</span>

</pre>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown">standards, including sustained inappropriate behavior,  harassment of an</span>

</pre>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown">individual, or aggression toward or disparagement of classes of individuals.</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Consequence**</span>: A permanent ban from any sort of public interaction within</span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown">the community.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Attribution</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown"></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown">This Code of Conduct is adapted from the <span class="p">[</span><span class="nv" style="color: #008080;">Contributor Covenant</span><span class="p">][</span><span class="ss" style="color: #990073;">homepage</span><span class="p">]</span>,</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown">version 2.0, available at</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown">https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown"></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown">Community Impact Guidelines were inspired by <span class="p">[</span><span class="nv" style="color: #008080;">Mozilla's code of conduct</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"><span class="nv" style="color: #008080;">enforcement ladder</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/mozilla/diversity</span><span class="p">)</span>.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">homepage</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://www.contributor-covenant.org</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown">For answers to common questions about this code of conduct, see the FAQ at</span>

</pre>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown">https://www.contributor-covenant.org/faq. Translations are available at</span>

</pre>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown">https://www.contributor-covenant.org/translations.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown"></span></pre>

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<br>

</li>

<li id="6651ddff6eb82c840ced7c1dddee15c6e1913dd4">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#6651ddff6eb82c840ced7c1dddee15c6e1913dd4"><strong>Dockerfile</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,15 +8,15 @@ ENV SHELL /bin/bash</td>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>/bin/bash <span class="nt" style="color: #000080;">-c</span> <span class="s2" style="color: #d14;">"install_packages wget bzip2 ca-certificates gnupg2 squashfs-tools git && </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="docker"><span class="s2" style="color: #d14;">    wget -O- https://neuro.debian.net/lists/xenial.us-ca.full > /etc/apt/sources.list.d/neurodebian.sources.list && </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="docker"><span class="s2" style="color: #d14;">    wget -O- https://neuro.debian.net/_static/neuro.debian.net.asc | apt-key add - && </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="docker"><span class="s2" style="color: #d14;">    install_packages singularity-container<span class="idiff left"> && </span></span><span class="se" style="color: #d14;"><span class="idiff right">\</span></span></span>

</pre>

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12

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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="docker"><span class="s2" style="color: #d14;"><span class="idiff left right">    </span>wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="docker"><span class="s2" style="color: #d14;">    install_packages singularity-container<span class="idiff left right">"</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="docker"><span class="k" style="font-weight: 600;"><span class="idiff left">RUN </span></span><span class="idiff">/bin/bash </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff right">"</span>wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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

13

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

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="docker"><span class="s2" style="color: #d14;">    bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="docker"><span class="s2" style="color: #d14;">    rm Miniconda3-latest-Linux-x86_64.sh<span class="idiff left"> && </span></span><span class="se" style="color: #d14;"><span class="idiff right">\</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="docker"><span class="s2" style="color: #d14;"><span class="idiff left right">    </span>conda install -y -c conda-forge mamba && </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="docker"><span class="s2" style="color: #d14;">    rm Miniconda3-latest-Linux-x86_64.sh<span class="idiff left right">"</span></span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="docker"><span class="k" style="font-weight: 600;"><span class="idiff left">RUN </span></span><span class="idiff">/bin/bash </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff right">"</span>conda install -y -c conda-forge mamba && </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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

16

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="docker"><span class="s2" style="color: #d14;">    mamba create -q -y -c conda-forge -c bioconda -n snakemake snakemake snakemake-minimal --only-deps && </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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

17

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

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="docker"><span class="s2" style="color: #d14;">    conda clean --all -y && </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="docker"><span class="s2" style="color: #d14;">    source activate snakemake && </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num 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">

19

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="docker"><span class="s2" style="color: #d14;">    which python && </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="docker"><span class="s2" style="color: #d14;">    pip install ."</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(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="LC20" class="line" lang="docker"><span class="s2" style="color: #d14;">    pip install .<span class="idiff left right">[reports,messaging,google-cloud]</span>"</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"source activate snakemake"</span> <span class="o" style="font-weight: 600;">></span> ~/.bashrc</span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> PATH /opt/conda/envs/snakemake/bin:${PATH}</span></span></pre>

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<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,6 +6,7 @@</td>

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

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Stack Overflow</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/stack-overflow-orange.svg</span><span class="p">)</span>](https://stackoverflow.com/questions/tagged/snakemake)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Twitter</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/twitter/follow/johanneskoester.svg?style=social&label=Follow</span><span class="p">)</span>](https://twitter.com/search?l=&q=%23snakemake%20from%3Ajohanneskoester)</span>

</pre>

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

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Github stars</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/stars/snakemake/snakemake?style=social</span><span class="p">)</span>](https://github.com/snakemake/snakemake/stargazers)</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Contributor Covenant</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg</span><span class="p">)</span>](code_of_conduct.md) </span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="gh" style="color: #999;"># Snakemake</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>

</pre>

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<br>

</li>

<li id="9983a3122073938d03b572d4b73df73fe03efe7d">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#9983a3122073938d03b572d4b73df73fe03efe7d"><strong>docs/_static/theme.css</strong></a>

The diff for this file was not included because it is too large.

<br>

</li>

<li id="254a2da7a740675e537439eb88e32083b9ea4771">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#254a2da7a740675e537439eb88e32083b9ea4771"><strong>docs/conf.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,8 +41,8 @@ extensions = [</td>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python">    <span class="s" style="color: #d14;">'sphinxarg.ext'</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(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="LC43" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">TODO enable once new theme is final</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># html_style = "theme.css"</span></span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">Snakemake theme (made by SciAni).</span></span></span>

</pre>

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

</td>

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

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="n" style="color: #333;"><span class="idiff left">html_css_files</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"theme.css"</span></span><span class="p"><span class="idiff right">]</span></span></span>

</pre>

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

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

46

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

<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any paths that contain templates here, relative to this directory.</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(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="LC48" class="line" lang="python"><span class="n" style="color: #333;">templates_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'_templates'</span><span class="p">]</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -153,7 +153,7 @@ html_static_path = ['_static']</td>

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

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any extra paths that contain custom files (such as robots.txt or</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># .htaccess) here, relative to this directory. These files are copied</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># directly to the root of the documentation.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_extra_path = []</span></span>

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_extra_path = [<span class="idiff left right">"_static/css"</span>]</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If not '', a 'Last updated on:' timestamp is inserted at every page bottom,</span></span>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># using the given strftime format.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="168" style="width: 35px; color: rgba(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="168" style="width: 35px; color: rgba(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">@@ -168,7 +168,7 @@ html_static_path = ['_static']</td>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Additional templates that should be rendered to pages, maps page names to</span></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># template names.</span></span>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_additional_pages = {}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_additional_pages = {<span class="idiff left right">"index": "index.html"</span>}</span></span>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="173" style="width: 35px; color: rgba(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="LC173" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If false, no module index is generated.</span></span>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_domain_indices = True</span></span>

</pre>

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<br>

</li>

<li id="7e143b2e3a88fc7b437114c03b2302f5afa981ec">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#7e143b2e3a88fc7b437114c03b2302f5afa981ec"><strong>docs/executing/cloud.rst</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="207" style="width: 35px; color: rgba(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="207" style="width: 35px; color: rgba(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">@@ -207,7 +207,7 @@ a full machine type:</td>

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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">.. code-block:: console</span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext">    --default-resources <span class="idiff left right">machine_type="</span>n1-standard"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">    --default-resources <span class="idiff left right">"machine_type=</span>n1-standard"</span>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext">If you want to specify the machine type as a resource, you can do that too:</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">@@ -330,4 +330,4 @@ When executing, Snakemake will make use of the defined resources and threads</td>

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="plaintext">to schedule jobs to the correct nodes. In particular, it will forward memory requirements</span>

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="plaintext">defined as `mem_mb` to Tibanna. Further, it will propagate the number of threads</span>

</pre>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="plaintext">a job intends to use, such that Tibanna can allocate it to the most cost-effective</span>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="plaintext">cloud compute instance available.</span></pre>

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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">cloud compute instance available.</span></pre>

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<br>

</li>

<li id="18336bcf377dc39d1fe1a9f38b710df68bb084fb">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#18336bcf377dc39d1fe1a9f38b710df68bb084fb"><strong>docs/executor_tutorial/azure_aks.rst</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.. _tutorial-azure-aks:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Auto-scaling Azure Kubernetes cluster without shared filesystem</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">In this tutorial we will show how to execute a Snakemake workflow</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">on an auto-scaling Azure Kubernetes cluster without a shared file-system.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">While Kubernetes is mainly known as microservice orchestration system with</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">self-healing properties, we will use it here simply as auto-scaling</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">compute orchestrator. One could use `persistent volumes in</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Kubernetes <https://docs.microsoft.com/en-us/azure/aks/azure-files-dynamic-pv>`__</span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">as shared file system, but this adds an unnecessary level of complexity</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">and most importantly costs. Instead we use cheap Azure Blob storage,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">which is used by Snakemake to automatically stage data in and out for</span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">every job.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Following the steps below you will</span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">#. set up Azure Blob storage, download the Snakemake tutorial data and upload to Azure</span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">#. then create an Azure Kubernetes (AKS) cluster</span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">#. and finally run the analysis with Snakemake on the cluster </span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Setup</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">:::::</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">To go through this tutorial, you need the following software installed:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">* Python_ ≥3.5</span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">* Snakemake_ ≥5.17</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">You should install conda as outlined in the :ref:`tutorial <tutorial-setup>`,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">and then install full snakemake with:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.. code:: console</span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">    conda create -c bioconda -c conda-forge -n snakemake snakemake</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Make sure that the ``kubernetes`` and ``azure-storage-blob`` modules are installed</span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">in this environment. Should they be missing install with:</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.. code:: console</span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">   pip install kubernetes</span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">   pip install azure-storage-blob</span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">In addition you will need the</span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">`Azure CLI command <https://docs.microsoft.com/en-us/cli/azure/install-azure-cli?view=azure-cli-latest>`__ </span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">installed.</span>

</pre>

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

</pre>

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

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Create an Azure storage account and upload data</span>

</pre>

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

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">We will be starting from scratch, i.e. we will </span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">create a new resource group and storage account. You can obviously reuse </span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">existing resources instead.</span>

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

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.. code:: console</span>

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

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">   # change the following names as required</span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">   # azure region where to run:</span>

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

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">   # name of the resource group to create:</span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">   resgroup=snakemaks-rg</span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">   # name of storage account to create (all lowercase, no hyphens etc.):</span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">   stgacct=snakemaksstg</span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">   # create a resource group with name and in region as defined above</span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">   az group create --name $resgroup --location $region</span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">   # create a general purpose storage account with cheapest SKU</span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">   az storage account create -n $stgacct -g $resgroup --sku Standard_LRS -l $region</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">Get a key for that account and save it as ``stgkey`` for later use:</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.. code:: console</span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">   stgkey=$(az storage account keys list -g $resgroup -n $storageacct | head -n1 | cut -f 3)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">Next, you will create a storage container (think: bucket) to upload the Snakemake tutorial data to:</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">.. code:: console</span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">   az storage container create --resource-group $resgroup --account-name $stgacct \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">       --account-key $stgkey --name snakemake-tutorial</span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">   cd /tmp</span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">   git clone https://github.com/snakemake/snakemake-tutorial-data.git</span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">   cd snakemake-tutorial-data</span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">   az storage blob upload-batch -d snakemake-tutorial --account-name $stgacct \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">       --account-key $stgkey -s data/ --destination-path data</span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">We are using `az storage blob` for uploading, because that `az` is already installed.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">A  more efficient way of uploading would be to use</span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">`azcopy <https://docs.microsoft.com/en-us/azure/storage/common/storage-use-azcopy-v10>`__.</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">Create an auto-scaling Kubernetes cluster</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">.. code:: console</span>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">   # change the cluster name as you like</span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">   clustername=snakemaks-aks</span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">   az aks create --resource-group $resgroup --name $clustername \</span>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">       --vm-set-type VirtualMachineScaleSets --load-balancer-sku standard --enable-cluster-autoscaler \</span>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">       --node-count 1 --min-count 1 --max-count 3 --node-vm-size Standard_D3_v2</span>

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

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">There is a lot going on here, so let’s unpack it: this creates an</span>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">`auto-scaling Kubernetes</span>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">cluster <https://docs.microsoft.com/en-us/azure/aks/cluster-autoscaler>`__</span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">(``--enable-cluster-autoscaler``) called ``$clustername`` (i.e. ``snakemaks-aks``), which starts</span>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">out with one node (``--node-count 1``) and has a maximum of three nodes</span>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">(``--min-count 1 --max-count 3``). For real world applications you will</span>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">want to increase the maximum count and also increase the VM size. You</span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">could for example choose a large instance from the DSv2 series and add a</span>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">larger disk with (``--node-osdisk-size``) if needed. See `here for more</span>

</pre>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">info on Linux VM</span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">sizes <https://docs.microsoft.com/en-us/azure/virtual-machines/linux/sizes>`__.</span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">Note, if you are creating the cluster in the Azure portal, click on the</span>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">ellipsis under node-pools to find the auto-scaling option.</span>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">Next, let’s fetch the credentials for this cluster, so that we can</span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">actually interact with it.</span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">.. code:: console</span>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">   az aks get-credentials --resource-group $resgroup --name $clustername</span>

</pre>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">   # print basic cluster info</span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">   kubectl cluster-info</span>

</pre>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">Running the workflow</span>

</pre>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">::::::::::::::::::::</span>

</pre>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">Below we will task Snakemake to install software on the fly with conda.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">For this we need a Snakefile with corresponding conda environment</span>

</pre>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">yaml files. You can download the package containing all those files `here <workflow/snakedir.zip>`__.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">After downloading, unzip it and cd into the newly created directory.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(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="LC140" class="line" lang="plaintext">.. code:: console</span>

</pre>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(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="LC142" class="line" lang="plaintext">   $ cd /tmp</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(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="LC143" class="line" lang="plaintext">   $ unzip ~/Downloads/snakedir.zip</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(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="LC144" class="line" lang="plaintext">   $ cd snakedir</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(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="LC145" class="line" lang="plaintext">   $ find .</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(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="LC146" class="line" lang="plaintext">   .</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(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="LC147" class="line" lang="plaintext">   ./Snakefile</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(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="LC148" class="line" lang="plaintext">   ./envs</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(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="LC149" class="line" lang="plaintext">   ./envs/calling.yaml</span>

</pre>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">   ./envs/mapping.yaml</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(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="LC152" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(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="LC153" class="line" lang="plaintext">Now, we will need to setup the credentials that allow the Kubernetes nodes to</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(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="LC154" class="line" lang="plaintext">read and write from blob storage. For the AzBlob storage provider in</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">Snakemake this is done through the environment variables</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(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="LC156" class="line" lang="plaintext">``AZ_BLOB_ACCOUNT_URL`` and optionally ``AZ_BLOB_CREDENTIAL``. See the</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(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="LC157" class="line" lang="plaintext">`documentation <snakefiles/remote_files.html#microsoft-azure-storage>`__ for more info.</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">``AZ_BLOB_ACCOUNT_URL`` takes the form</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(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="LC159" class="line" lang="plaintext">``https://<accountname>.blob.core.windows.net`` and may also contain a</span>

</pre>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">shared access signature (SAS), which is a powerful way to define fine grained</span>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">and even time controlled access to storage on Azure. The SAS can be part of the</span>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">URL, but if it’s missing, then you can set it with</span>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">``AZ_BLOB_CREDENTIAL`` or alternatively use the storage account key. To</span>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">keep things simple we’ll use the storage key here, since we already have it available,</span>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">but a SAS is generally more powerful. We’ll pass those variables on to the Kubernetes</span>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">with ``--envvars`` (see below).</span>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">Now you are ready to run the analysis:</span>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">.. code:: console</span>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">   export AZ_BLOB_ACCOUNT_URL="https://${stgacct}.blob.core.windows.net"</span>

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">   export AZ_BLOB_CREDENTIAL="$stgkey"</span>

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">   snakemake --kubernetes \</span>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">       --default-remote-prefix snakemake-tutorial --default-remote-provider AzBlob \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">       --envvars AZ_BLOB_ACCOUNT_URL AZ_BLOB_CREDENTIAL --use-conda --jobs 3</span>

</pre>

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">This will use the default Snakemake image from Dockerhub. If you would like to use your</span>

</pre>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">own, make sure that the image contains the same Snakemake version as installed locally</span>

</pre>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">and also supports Azure Blob storage. If you plan to use your own image hosted on</span>

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> Azure Container Registries (ACR), make sure to attach the ACR to your Kubernetes </span>

</pre>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> cluster. See `here <https://docs.microsoft.com/en-us/azure/aks/cluster-container-registry-integration>`__ for more info.</span>

</pre>

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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">While Snakemake is running the workflow, it prints handy debug</span>

</pre>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">statements per job, e.g.:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">.. code:: console</span>

</pre>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">   kubectl describe pod snakejob-c4d9bf9e-9076-576b-a1f9-736ec82afc64</span>

</pre>

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">   kubectl logs snakejob-c4d9bf9e-9076-576b-a1f9-736ec82afc64</span>

</pre>

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">With these you can also follow the scale-up of the cluster:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">.. code:: console</span>

</pre>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">   Events:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">   Type     Reason             Age                From                Message</span>

</pre>

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">   ----     ------             ----               ----                -------</span>

</pre>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">   Warning  FailedScheduling   60s (x3 over 62s)  default-scheduler   0/1 nodes are available: 1 Insufficient cpu.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">   Normal   TriggeredScaleUp   50s                cluster-autoscaler  pod triggered scale-up: [{aks-nodepool1-17839284-vmss 1->3 (max: 3)}]</span>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">After a while you will see three nodes (each running one BWA job), which</span>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">was defined as the maximum above while creating your Kubernetes cluster:</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">.. code:: console</span>

</pre>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">   $ kubectl get nodes</span>

</pre>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">   NAME                                STATUS   ROLES   AGE   VERSION</span>

</pre>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">   aks-nodepool1-17839284-vmss000000   Ready    agent   74m   v1.15.11</span>

</pre>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">   aks-nodepool1-17839284-vmss000001   Ready    agent   11s   v1.15.11</span>

</pre>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">   aks-nodepool1-17839284-vmss000002   Ready    agent   62s   v1.15.11</span>

</pre>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">To get detailed information including historical data about used</span>

</pre>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">resources, check Insights in the Azure portal under your AKS cluster</span>

</pre>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">Monitoring/Insights. The alternative is an instant snapshot on the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">command line:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">::</span>

</pre>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">   $ kubectl top node</span>

</pre>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">   NAME                                CPU(cores)   CPU%   MEMORY(bytes)   MEMORY%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">   aks-nodepool1-17839284-vmss000000   217m         5%     1796Mi          16%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">   aks-nodepool1-17839284-vmss000001   1973m        51%    529Mi           4%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">   aks-nodepool1-17839284-vmss000002   698m         18%    1485Mi          13%</span>

</pre>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">After completion all results including</span>

</pre>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">logs can be found in the blob container. You will also find results</span>

</pre>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">listed in the first Snakefile target downloaded to the working directoy.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">::</span>

</pre>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">   $ find snakemake-tutorial/</span>

</pre>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">   snakemake-tutorial/</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">   snakemake-tutorial/calls</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="236" style="width: 35px; color: rgba(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="LC236" class="line" lang="plaintext">   snakemake-tutorial/calls/all.vcf</span>

</pre>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">   $ az storage blob list  --container-name snakemake-tutorial --account-name $stgacct --account-key $stgkey -o table</span>

</pre>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">   Name                     Blob Type    Blob Tier    Length    Content Type                       Last Modified              Snapshot</span>

</pre>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">   -----------------------  -----------  -----------  --------  ---------------------------------  -------------------------  ----------</span>

</pre>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">   calls/all.vcf            BlockBlob    Hot          90986     application/octet-stream           2020-06-08T05:11:31+00:00</span>

</pre>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">   data/genome.fa           BlockBlob    Hot          234112    application/octet-stream           2020-06-08T03:26:54+00:00</span>

</pre>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">   # etc.</span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">   logs/mapped_reads/A.log  BlockBlob    Hot          346       application/octet-stream           2020-06-08T04:59:50+00:00</span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">   mapped_reads/A.bam       BlockBlob    Hot          2258058   application/octet-stream           2020-06-08T04:59:50+00:00</span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">   sorted_reads/A.bam       BlockBlob    Hot          2244660   application/octet-stream           2020-06-08T05:03:41+00:00</span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">   sorted_reads/A.bam.bai   BlockBlob    Hot          344       application/octet-stream           2020-06-08T05:06:25+00:00</span>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">   # same for samples B and C</span>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext">Now that the execution is complete, the AKS cluster will scale down</span>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext">automatically. If you are not planning to run anything else, it makes</span>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">sense to shut down it down entirely:</span>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">::</span>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">   az aks delete --name akscluster --resource-group $resgroup</span>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"></span></pre>

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<br>

</li>

<li id="a51db43db8671eca05cb09411a68924732699541">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#a51db43db8671eca05cb09411a68924732699541"><strong>docs/executor_tutorial/google_lifesciences.rst</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,12 +17,33 @@ To go through this tutorial, you need the following software installed:</td>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">Snakemake_</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">≥</span><span class="m" style="color: #099;">5.16</span></span>

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">git</span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="mosel"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="mosel"><span class="n" style="color: #333;">You</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">install</span> <span class="n" style="color: #333;">conda</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outlined</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="p">:</span><span class="n" style="color: #333;">ref</span><span class="p">:`</span><span class="n" style="color: #333;">tutorial</span> <span class="p"><</span><span class="n" style="color: #333;">tutorial</span><span class="p">-</span><span class="n" style="color: #333;">setup</span><span class="p">>`,</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">install</span> <span class="n" style="color: #333;">full</span> <span class="n" style="color: #333;">snakemake</span> <span class="k" style="font-weight: 600;">with</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(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="LC20" class="line" lang="mosel"><span class="n" style="color: #333;">First</span><span class="p">,</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">have</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">install</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Miniconda</span> <span class="n" style="color: #333;">Python3</span> <span class="n" style="color: #333;">distribution</span><span class="p">.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(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="LC21" class="line" lang="mosel"><span class="n" style="color: #333;">See</span> <span class="p">`</span><span class="n" style="color: #333;">here</span> <span class="p"><</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">conda</span><span class="p">.</span><span class="n" style="color: #333;">io</span><span class="p">/</span><span class="n" style="color: #333;">en</span><span class="p">/</span><span class="n" style="color: #333;">latest</span><span class="p">/</span><span class="n" style="color: #333;">miniconda</span><span class="p">.</span><span class="n" style="color: #333;">html</span><span class="p">>`</span><span class="n" style="color: #333;">_</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">installation</span> <span class="n" style="color: #333;">instructions</span><span class="p">.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(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="LC22" class="line" lang="mosel"><span class="n" style="color: #333;">Make</span> <span class="n" style="color: #333;">sure</span> <span class="k" style="font-weight: 600;">to</span> <span class="p">...</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="mosel"><span class="p">..</span> <span class="n" style="color: #333;">code</span><span class="p">::</span> <span class="n" style="color: #333;">console</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">Install</span> <span class="n" style="color: #333;">the</span> <span class="p">**</span><span class="n" style="color: #333;">Python</span> <span class="m" style="color: #099;">3</span><span class="p">**</span> <span class="k" style="font-weight: 600;">version</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Miniconda</span><span class="p">.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">Answer</span> <span class="n" style="color: #333;">yes</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">question</span> <span class="n" style="color: #333;">whether</span> <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">shall</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">put</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">PATH</span><span class="p">.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">default</span> <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">solver</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">bit</span> <span class="n" style="color: #333;">slow</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sometimes</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">issues</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">`</span><span class="n" style="color: #333;">selecting</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">latest</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">releases</span> <span class="p"><</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">conda</span><span class="p">/</span><span class="n" style="color: #333;">conda</span><span class="p">/</span><span class="n" style="color: #333;">issues</span><span class="p">/</span><span class="m" style="color: #099;">9905</span><span class="p">>`</span><span class="n" style="color: #333;">_</span><span class="p">.</span> <span class="n" style="color: #333;">Therefore</span><span class="p">,</span> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">recommend</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">install</span> <span class="p">`</span><span class="n" style="color: #333;">Mamba</span> <span class="p"><</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">QuantStack</span><span class="p">/</span><span class="n" style="color: #333;">mamba</span><span class="p">>`</span><span class="n" style="color: #333;">_</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">drop</span><span class="p">-</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">replacement</span> <span class="n" style="color: #333;">via</span></span>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="mosel"><span class="p">..</span> <span class="n" style="color: #333;">code</span><span class="p">-</span><span class="n" style="color: #333;">block</span><span class="p">::</span> <span class="n" style="color: #333;">console</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="mosel">    <span class="p">$</span> <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">install</span> <span class="p">-</span><span class="n" style="color: #333;">c</span> <span class="n" style="color: #333;">conda</span><span class="p">-</span><span class="n" style="color: #333;">forge</span> <span class="n" style="color: #333;">mamba</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

</pre>

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

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Then</span><span class="p">,</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">install</span> <span class="n" style="color: #333;">Snakemake</span> <span class="k" style="font-weight: 600;">with</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

<pre style="margin: 0;">+<span id="LC34" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

35

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

<pre style="margin: 0;">+<span id="LC35" class="line" lang="mosel"><span class="p">..</span> <span class="n" style="color: #333;">code</span><span class="p">-</span><span class="n" style="color: #333;">block</span><span class="p">::</span> <span class="n" style="color: #333;">console</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel">    <span class="p">$</span> <span class="n" style="color: #333;">mamba</span> <span class="nb" style="color: #0086b3;">create</span> <span class="p">-</span><span class="n" style="color: #333;">c</span> <span class="n" style="color: #333;">conda</span><span class="p">-</span><span class="n" style="color: #333;">forge</span> <span class="p">-</span><span class="n" style="color: #333;">c</span> <span class="n" style="color: #333;">bioconda</span> <span class="p">-</span><span class="n" style="color: #333;">n</span> <span class="n" style="color: #333;">snakemake</span> <span class="n" style="color: #333;">snakemake</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel"><span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="p">`</span><span class="n" style="color: #333;">Bioconda</span> <span class="p"><</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">bioconda</span><span class="p">.</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">io</span><span class="p">>`</span><span class="n" style="color: #333;">_</span> <span class="n" style="color: #333;">channel</span><span class="p">.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">install</span> <span class="n" style="color: #333;">snakemake</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">isolated</span> <span class="n" style="color: #333;">software</span> <span class="n" style="color: #333;">environment</span><span class="p">,</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">has</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">activated</span> <span class="k" style="font-weight: 600;">with</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel"><span class="p">..</span> <span class="n" style="color: #333;">code</span><span class="p">-</span><span class="n" style="color: #333;">block</span><span class="p">::</span> <span class="n" style="color: #333;">console</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel">    <span class="p">$</span> <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">activate</span> <span class="n" style="color: #333;">snakemake</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

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

<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel">    <span class="p">$</span> <span class="n" style="color: #333;">snakemake</span> <span class="p">--</span><span class="n" style="color: #333;">help</span></span>

</pre>

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

24

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

46

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

<pre style="margin: 0;"> <span id="LC46" class="line" lang="mosel"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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

</td>

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

<pre style="margin: 0;">-<span id="LC25" class="line" lang="mosel">    <span class="n" style="color: #333;">conda</span> <span class="nb" style="color: #0086b3;">create</span> <span class="p">-</span><span class="n" style="color: #333;">c</span> <span class="n" style="color: #333;">bioconda</span> <span class="p">-</span><span class="n" style="color: #333;">c</span> <span class="n" style="color: #333;">conda</span><span class="p">-</span><span class="n" style="color: #333;">forge</span> <span class="p">-</span><span class="n" style="color: #333;">n</span> <span class="n" style="color: #333;">snakemake</span> <span class="n" style="color: #333;">snakemake</span></span>

</pre>

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

26

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

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

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

48

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

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

<pre style="margin: 0;"> <span id="LC49" class="line" lang="mosel"><span class="n" style="color: #333;">Credentials</span></span>

</pre>

</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">@@ -73,7 +94,7 @@ If you wanted to upload to a "subfolder" path in a bucket, you would do that as</td>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="mosel"><span class="s1" style="color: #d14;">.. code:: console</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="mosel"></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="mosel"><span class="s1" style="color: #d14;">    export GOOGLE_APPLICATION_CREDENTIALS="/path/to/credentials.json"</span></span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="mosel"><span class="s1" style="color: #d14;">    python upload_google_storage.py snakemake-testing-data/subfolder</span></span>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="mosel"><span class="s1" style="color: #d14;">    python upload_google_storage.py snakemake-testing-data/subfolder<span class="idiff left right"> data/</span></span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="mosel"></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="mosel"><span class="s1" style="color: #d14;">Your bucket (and the folder prefix) will be referred to as the</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="mosel"><span class="s1" style="color: #d14;">`--default-remote-prefix` when you run snakemake. You can visually</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="89" style="width: 35px; color: rgba(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="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,8 +110,9 @@ Step 2: Write your Snakefile, Environment File, and Scripts</td>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="mosel"><span class="s1" style="color: #d14;">Now that we'</span><span class="n" style="color: #333;">ve</span> <span class="n" style="color: #333;">exported</span> <span class="n" style="color: #333;">our</span> <span class="n" style="color: #333;">credentials</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">dependencies</span> <span class="n" style="color: #333;">installed</span><span class="p">,</span> <span class="n" style="color: #333;">let</span><span class="s1" style="color: #d14;">'s</span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="mosel"><span class="s1" style="color: #d14;">get our workflow! This is the exact same workflow from the :ref:`basic tutorial<tutorial-basics>`,</span></span>

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<td class="diff-line-num new_line" data-linenumber="112" style="width: 35px; color: rgba(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="LC112" class="line" lang="mosel"><span class="s1" style="color: #d14;">so if you need a refresher on the design or basics, please see those pages.</span></span>

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="mosel"><span class="s1" style="color: #d14;">We won'</span><span class="n" style="color: #333;">t</span> <span class="n" style="color: #333;">need</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">clone</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">from</span> <span class="p">`</span><span class="n" style="color: #333;">snakemake</span><span class="p">-</span><span class="n" style="color: #333;">tutorial</span><span class="p">-</span><span class="n" style="color: #333;">data</span> <span class="p"><</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">snakemake</span><span class="p">/</span><span class="n" style="color: #333;">snakemake</span><span class="p">-</span><span class="n" style="color: #333;">tutorial</span><span class="p">-</span><span class="n" style="color: #333;">data</span><span class="p">>`</span><span class="n" style="color: #333;">_</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="mosel"><span class="n" style="color: #333;">because</span> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">publicly</span> <span class="n" style="color: #333;">accessible</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">Google</span> <span class="n" style="color: #333;">Storage</span><span class="p">.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="mosel"><span class="s1" style="color: #d14;">You can find the Snakefile, supporting scripts for plotting and environment in the</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="mosel"><span class="s1" style="color: #d14;"> `snakemake-tutorial-data <https://github.com/snakemake/snakemake-tutorial-data>`_</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="mosel"><span class="s1" style="color: #d14;">repository.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="mosel"></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="mosel"><span class="s1" style="color: #d14;">First, how does a working directory work for this executor? The present</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="mosel"><span class="s1" style="color: #d14;">working directory, as identified by Snakemake that has the Snakefile, and where</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,9 +124,9 @@ package includes the .snakemake folder that would have been generated locally.</td>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="mosel"><span class="s1" style="color: #d14;">The build package is then downloaded and extracted by each cloud executor, which</span></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="mosel"><span class="s1" style="color: #d14;">is a Google Compute instance.</span></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="mosel"></span>

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<td class="diff-line-num old old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="mosel"><span class="n" style="color: #333;">We</span> <span class="k" style="font-weight: 600;">next</span> <span class="n" style="color: #333;">need</span> <span class="n" style="color: #333;">an</span> <span class="p">`</span><span class="n" style="color: #333;">environment</span><span class="p">.</span><span class="n" style="color: #333;">yml</span><span class="p">`</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">define</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">dependencies</span></span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="mosel"><span class="s1" style="color: #d14;">We next need an `environment.y<span class="idiff left right">a</span>ml` file that will define the dependencies</span></span>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="mosel"><span class="s1" style="color: #d14;">that we want installed with conda for our job. If you cloned the "snakemake-tutorial-data"</span></span>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="mosel"><span class="n" style="color: #333;">repository</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">already</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">this</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">good</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">go</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="k" style="font-weight: 600;">not</span><span class="p">,</span> <span class="n" style="color: #333;">save</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">to</span> <span class="p">`</span><span class="n" style="color: #333;">environment</span><span class="p">.</span><span class="n" style="color: #333;">yml</span><span class="p">`</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="mosel"><span class="s1" style="color: #d14;">repository you will already have this, and you are good to go. If not, save this to `environment.y<span class="idiff left right">a</span>ml`</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="mosel"><span class="s1" style="color: #d14;">in your working directory:</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="mosel"></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="mosel"><span class="s1" style="color: #d14;">.. code:: yaml</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="146" style="width: 35px; color: rgba(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">@@ -124,13 +146,13 @@ in your working directory:</td>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="mosel"><span class="s1" style="color: #d14;">      - pysam =0.15.0</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="mosel"><span class="s1" style="color: #d14;">    </span></span>

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

</pre>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="mosel"><span class="n" style="color: #333;">Notice</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">reference</span> <span class="n" style="color: #333;">this</span> <span class="p">`</span><span class="n" style="color: #333;">environment</span><span class="p">.</span><span class="n" style="color: #333;">yml</span><span class="p">`</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Snakefile</span> <span class="n" style="color: #333;">below</span><span class="p">.</span></span>

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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(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="LC149" class="line" lang="mosel"><span class="s1" style="color: #d14;">Notice that we reference this `environment.y<span class="idiff left right">a</span>ml` file in the Snakefile below.</span></span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="mosel"><span class="s1" style="color: #d14;">Importantly, if you were optimizing a pipeline, you would likely have a folder</span></span>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="mosel"><span class="s1" style="color: #d14;">"envs" with more than one environment specification, one for each step.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="mosel"><span class="s1" style="color: #d14;">This workflow uses the same environment (with many dependencies) instead of</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="mosel"><span class="s1" style="color: #d14;">this strategy to minimize the number of files for you.</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="mosel"></span>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">Snakefile</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">content</span><span class="p">.</span> <span class="n" style="color: #333;">It</span><span class="s1" style="color: #d14;">'s important to note</span></span>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="mosel"><span class="s1" style="color: #d14;">The Snakefile <span class="idiff left right">(also included in the repository) </span>then has the following content. It'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">important</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">note</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="mosel"><span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">have</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">customized</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">basic</span> <span class="n" style="color: #333;">tutorial</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">hard</span> <span class="n" style="color: #333;">code</span> </span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="mosel"><span class="n" style="color: #333;">any</span> <span class="n" style="color: #333;">storage</span><span class="p">.</span> <span class="n" style="color: #333;">We</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">telling</span> <span class="n" style="color: #333;">snakemake</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">remote</span> <span class="n" style="color: #333;">bucket</span> <span class="k" style="font-weight: 600;">as</span> </span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="mosel"><span class="n" style="color: #333;">storage</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">local</span> <span class="n" style="color: #333;">filesystem</span><span class="p">.</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="167" style="width: 35px; color: rgba(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">@@ -145,16 +167,16 @@ storage instead of the local filesystem.</td>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="mosel"></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="mosel">    <span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">bwa_map</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="mosel">        <span class="n" style="color: #333;">input</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="mosel"><span class="s1" style="color: #d14;">        fastq="samples/{sample}.fastq",</span></span>

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="mosel"><span class="s1" style="color: #d14;">        idx=multiext("genome.fa", ".amb", ".ann", ".bwt", ".pac", ".sa")</span></span>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="mosel"><span class="s1" style="color: #d14;">    conda:</span></span>

</pre>

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

151

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">"environment.y</span>ml"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

152

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<td class="diff-line-num new_line old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="mosel"><span class="s1" style="color: #d14;">    output:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

153

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="mosel"><span class="s1" style="color: #d14;">        "mapped_reads/{sample}.bam"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

154

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="mosel"><span class="s1" style="color: #d14;">    params:</span></span>

</pre>

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

155

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<td class="diff-line-num new_line old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="mosel"><span class="s1" style="color: #d14;">        idx=lambda w, input: os.path.splitext(input.idx[0])[0]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

156

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<td class="diff-line-num new_line old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="mosel"><span class="s1" style="color: #d14;">    shell:</span></span>

</pre>

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

157

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="mosel"><span class="s1" style="color: #d14;">        "bwa mem {params.idx} {input.fastq} | samtools view -Sb - > {output}"</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(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="LC170" class="line" lang="mosel">        <span class="idiff left right">    </span><span class="n" style="color: #333;">fastq</span><span class="p">=</span><span class="s2" style="color: #d14;">"samples/{sample}.fastq"</span><span class="p">,</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(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="LC171" class="line" lang="mosel">        <span class="idiff left right">    </span><span class="n" style="color: #333;">idx</span><span class="p">=</span><span class="n" style="color: #333;">multiext</span><span class="p">(</span><span class="s2" style="color: #d14;">"genome.fa"</span><span class="p">,</span> <span class="s2" style="color: #d14;">".amb"</span><span class="p">,</span> <span class="s2" style="color: #d14;">".ann"</span><span class="p">,</span> <span class="s2" style="color: #d14;">".bwt"</span><span class="p">,</span> <span class="s2" style="color: #d14;">".pac"</span><span class="p">,</span> <span class="s2" style="color: #d14;">".sa"</span><span class="p">)</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(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="LC172" class="line" lang="mosel">    <span class="idiff left right">    </span><span class="n" style="color: #333;">conda</span><span class="p">:</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(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="LC173" class="line" lang="mosel">        <span class="idiff left">    </span><span class="s2" style="color: #d14;"><span class="idiff right">"environment.ya</span>ml"</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(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="LC174" class="line" lang="mosel">    <span class="idiff left right">    </span><span class="n" style="color: #333;">output</span><span class="p">:</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(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="LC175" class="line" lang="mosel">        <span class="idiff left right">    </span><span class="s2" style="color: #d14;">"mapped_reads/{sample}.bam"</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(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="LC176" class="line" lang="mosel">    <span class="idiff left right">    </span><span class="n" style="color: #333;">params</span><span class="p">:</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(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="LC177" class="line" lang="mosel">        <span class="idiff left right">    </span><span class="n" style="color: #333;">idx</span><span class="p">=</span><span class="n" style="color: #333;">lambda</span> <span class="n" style="color: #333;">w</span><span class="p">,</span> <span class="n" style="color: #333;">input</span><span class="p">:</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">idx</span><span class="p">[</span><span class="m" style="color: #099;">0</span><span class="p">])[</span><span class="m" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(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="LC178" class="line" lang="mosel">    <span class="idiff left right">    </span><span class="n" style="color: #333;">shell</span><span class="p">:</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(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="LC179" class="line" lang="mosel">        <span class="idiff left right">    </span><span class="s2" style="color: #d14;">"bwa mem {params.idx} {input.fastq} | samtools view -Sb - > {output}"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="mosel"></span>

</pre>

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

159

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<td class="diff-line-num new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

181

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="mosel">    <span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">samtools_sort</span><span class="p">:</span></span>

</pre>

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

160

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<td class="diff-line-num new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

182

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="mosel">        <span class="n" style="color: #333;">input</span><span class="p">:</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -162,7 +184,7 @@ storage instead of the local filesystem.</td>

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

162

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<td class="diff-line-num new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

184

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="mosel">        <span class="n" style="color: #333;">output</span><span class="p">:</span></span>

</pre>

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

163

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<td class="diff-line-num new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

185

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"sorted_reads/{sample}.bam"</span></span>

</pre>

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

164

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<td class="diff-line-num new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

186

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="mosel">        <span class="n" style="color: #333;">conda</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

165

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<td class="diff-line-num new_line old" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="mosel"><span class="s1" style="color: #d14;">            "environment.yml"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

187

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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="LC187" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"environment.y<span class="idiff left right">a</span>ml"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

166

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<td class="diff-line-num new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

188

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="mosel">        <span class="n" style="color: #333;">shell</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

167

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<td class="diff-line-num new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

189

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"samtools sort -T sorted_reads/{wildcards.sample} "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

168

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<td class="diff-line-num new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

190

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"-O bam {input} > {output}"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="173" style="width: 35px; color: rgba(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="195" style="width: 35px; color: rgba(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">@@ -173,7 +195,7 @@ storage instead of the local filesystem.</td>

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<td class="diff-line-num old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

173

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<td class="diff-line-num new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

195

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="mosel">        <span class="n" style="color: #333;">output</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

174

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<td class="diff-line-num new_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">

196

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"sorted_reads/{sample}.bam.bai"</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

175

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<td class="diff-line-num new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

197

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="mosel">        <span class="n" style="color: #333;">conda</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

176

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<td class="diff-line-num new_line old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC176" class="line" lang="mosel"><span class="s1" style="color: #d14;">            "environment.yml"</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

198

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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="LC198" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"environment.y<span class="idiff left right">a</span>ml"</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

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<td class="diff-line-num new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

199

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="mosel">        <span class="n" style="color: #333;">shell</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

178

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<td class="diff-line-num new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

200

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

<pre style="margin: 0;"> <span id="LC200" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"samtools index {input}"</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

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<td class="diff-line-num new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="mosel"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="207" style="width: 35px; color: rgba(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">@@ -185,7 +207,7 @@ storage instead of the local filesystem.</td>

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<td class="diff-line-num old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="207" style="width: 35px; color: rgba(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="LC207" class="line" lang="mosel">        <span class="n" style="color: #333;">output</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="208" style="width: 35px; color: rgba(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="LC208" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"calls/all.vcf"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="209" style="width: 35px; color: rgba(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="LC209" class="line" lang="mosel">        <span class="n" style="color: #333;">conda</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="mosel"><span class="s1" style="color: #d14;">            "environment.yml"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"environment.y<span class="idiff left right">a</span>ml"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="211" style="width: 35px; color: rgba(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="LC211" class="line" lang="mosel">        <span class="n" style="color: #333;">shell</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="212" style="width: 35px; color: rgba(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="LC212" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"samtools mpileup -g -f {input.fa} {input.bam} | "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="213" style="width: 35px; color: rgba(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="LC213" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"bcftools call -mv - > {output}"</span></span>

</pre>

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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>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="218" style="width: 35px; color: rgba(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">@@ -196,18 +218,22 @@ storage instead of the local filesystem.</td>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="218" style="width: 35px; color: rgba(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="LC218" class="line" lang="mosel">        <span class="n" style="color: #333;">output</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(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="LC219" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"plots/quals.svg"</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="220" style="width: 35px; color: rgba(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="LC220" class="line" lang="mosel">        <span class="n" style="color: #333;">conda</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="mosel"><span class="s1" style="color: #d14;">            "environment.yml"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"environment.y<span class="idiff left right">a</span>ml"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="222" style="width: 35px; color: rgba(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="LC222" class="line" lang="mosel">        <span class="n" style="color: #333;">script</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="223" style="width: 35px; color: rgba(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="LC223" class="line" lang="mosel">            <span class="s2" style="color: #d14;">"plot-quals.py"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="224" style="width: 35px; color: rgba(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="LC224" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

225

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="mosel"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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">

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="mosel"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="mosel"><span class="s1" style="color: #d14;">And let'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">also</span> <span class="nb" style="color: #0086b3;">write</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">script</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">our</span> <span class="n" style="color: #333;">present</span> <span class="n" style="color: #333;">working</span> <span class="n" style="color: #333;">directory</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">last</span> <span class="n" style="color: #333;">step</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="mosel"><span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">plotting</span> <span class="p">-</span> <span class="n" style="color: #333;">call</span> <span class="n" style="color: #333;">this</span> <span class="p">`</span><span class="n" style="color: #333;">plot</span><span class="p">-</span><span class="n" style="color: #333;">quals</span><span class="p">.</span><span class="n" style="color: #333;">py</span><span class="p">`:</span></span>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="227" style="width: 35px; color: rgba(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="LC227" class="line" lang="mosel"><span class="k" style="font-weight: 600;">And</span> <span class="n" style="color: #333;">make</span> <span class="n" style="color: #333;">sure</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">script</span> <span class="p">`</span><span class="n" style="color: #333;">plot</span><span class="p">-</span><span class="n" style="color: #333;">quals</span><span class="p">.</span><span class="n" style="color: #333;">py</span><span class="p">`</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">your</span> <span class="n" style="color: #333;">present</span> <span class="n" style="color: #333;">working</span> <span class="n" style="color: #333;">directory</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">last</span> <span class="n" style="color: #333;">step</span><span class="p">.</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="228" style="width: 35px; color: rgba(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="LC228" class="line" lang="mosel"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">script</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">help</span> <span class="n" style="color: #333;">us</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">plotting</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">included</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> </span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="229" style="width: 35px; color: rgba(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="LC229" class="line" lang="mosel"> <span class="p">`</span><span class="n" style="color: #333;">snakemake</span><span class="p">-</span><span class="n" style="color: #333;">tutorial</span><span class="p">-</span><span class="n" style="color: #333;">data</span> <span class="p"><</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">snakemake</span><span class="p">/</span><span class="n" style="color: #333;">snakemake</span><span class="p">-</span><span class="n" style="color: #333;">tutorial</span><span class="p">-</span><span class="n" style="color: #333;">data</span><span class="p">>`</span><span class="n" style="color: #333;">_</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="230" style="width: 35px; color: rgba(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="LC230" class="line" lang="mosel"><span class="n" style="color: #333;">repository</span><span class="p">.</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="231" style="width: 35px; color: rgba(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="LC231" class="line" lang="mosel"></span>

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<td class="diff-line-num new_line" data-linenumber="232" style="width: 35px; color: rgba(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="LC232" class="line" lang="mosel"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="mosel"><span class="p">..</span> <span class="n" style="color: #333;">code</span><span class="p">::</span> <span class="n" style="color: #333;">python</span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="mosel"></span>

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<td class="diff-line-num new_line" data-linenumber="235" style="width: 35px; color: rgba(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="LC235" class="line" lang="mosel">    <span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">matplotlib</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="236" style="width: 35px; color: rgba(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="LC236" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="237" style="width: 35px; color: rgba(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="LC237" class="line" lang="mosel">    <span class="n" style="color: #333;">matplotlib</span><span class="p">.</span><span class="n" style="color: #333;">use</span><span class="p">(</span><span class="s2" style="color: #d14;">"Agg"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="238" style="width: 35px; color: rgba(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="LC238" class="line" lang="mosel">    <span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">matplotlib</span><span class="p">.</span><span class="n" style="color: #333;">pyplot</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">plt</span></span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="mosel">    <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">pysam</span> <span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">VariantFile</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="491" style="width: 35px; color: rgba(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="517" style="width: 35px; color: rgba(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">@@ -491,7 +517,7 @@ Step 5: Debugging</td>

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<td class="diff-line-num old_line" data-linenumber="491" style="width: 35px; color: rgba(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="LC517" class="line" lang="mosel"><span class="p">:::::::::::::::::</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC518" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="mosel"><span class="n" style="color: #333;">Let</span><span class="s1" style="color: #d14;">'s introduce an error (purposefully) into our Snakefile to practice debugging.</span></span>

</pre>

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494

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<td class="diff-line-num new_line old" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC494" class="line" lang="mosel"><span class="s1" style="color: #d14;">Let'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">remove</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">environment</span><span class="p">.</span><span class="n" style="color: #333;">yml</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">rule</span><span class="p">,</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">would</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

520

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<pre style="margin: 0;">+<span id="LC520" class="line" lang="mosel"><span class="s1" style="color: #d14;">Let'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">remove</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">environment</span><span class="p">.</span><span class="n" style="color: #333;">y<span class="idiff left right">a</span>ml</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">first</span> <span class="n" style="color: #333;">rule</span><span class="p">,</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">would</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

495

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<td class="diff-line-num new_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

521

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<pre style="margin: 0;"> <span id="LC521" class="line" lang="mosel"><span class="n" style="color: #333;">expect</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">Snakemake</span> <span class="n" style="color: #333;">won</span><span class="s1" style="color: #d14;">'t be able to find the executables for bwa and samtools.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

496

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<td class="diff-line-num new_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

522

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<pre style="margin: 0;"> <span id="LC522" class="line" lang="mosel"><span class="s1" style="color: #d14;">In your Snakefile, change this:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

497

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<td class="diff-line-num new_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

523

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<pre style="margin: 0;"> <span id="LC523" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="499" style="width: 35px; color: rgba(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="525" style="width: 35px; color: rgba(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">@@ -499,16 +525,16 @@ In your Snakefile, change this:</td>

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<td class="diff-line-num old_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

499

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<td class="diff-line-num new_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

525

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<pre style="margin: 0;"> <span id="LC525" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

500

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<td class="diff-line-num new_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

526

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<pre style="margin: 0;"> <span id="LC526" class="line" lang="mosel"><span class="s1" style="color: #d14;">    rule bwa_map:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

501

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<td class="diff-line-num new_line" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

527

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<pre style="margin: 0;"> <span id="LC527" class="line" lang="mosel"><span class="s1" style="color: #d14;">        input:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

502

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<td class="diff-line-num new_line old" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC502" class="line" lang="mosel"><span class="s1" style="color: #d14;">        fastq="samples/{sample}.fastq",</span></span>

</pre>

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503

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<td class="diff-line-num new_line old" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC503" class="line" lang="mosel"><span class="s1" style="color: #d14;">        idx=multiext("genome.fa", ".amb", ".ann", ".bwt", ".pac", ".sa")</span></span>

</pre>

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504

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<td class="diff-line-num new_line old" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC504" class="line" lang="mosel"><span class="s1" style="color: #d14;">    conda:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

505

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<td class="diff-line-num new_line old" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC505" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">"environment.y</span>ml"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

506

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<td class="diff-line-num new_line old" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC506" class="line" lang="mosel"><span class="s1" style="color: #d14;">    output:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

507

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<td class="diff-line-num new_line old" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC507" class="line" lang="mosel"><span class="s1" style="color: #d14;">        "mapped_reads/{sample}.bam"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

508

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<td class="diff-line-num new_line old" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC508" class="line" lang="mosel"><span class="s1" style="color: #d14;">    params:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

509

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<td class="diff-line-num new_line old" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC509" class="line" lang="mosel"><span class="s1" style="color: #d14;">        idx=lambda w, input: os.path.splitext(input.idx[0])[0]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

510

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<td class="diff-line-num new_line old" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC510" class="line" lang="mosel"><span class="s1" style="color: #d14;">    shell:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

511

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<td class="diff-line-num new_line old" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC511" class="line" lang="mosel"><span class="s1" style="color: #d14;">        "bwa mem {params.idx} {input.fastq} | samtools view -Sb - > {output}"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

528

</td>

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

<pre style="margin: 0;">+<span id="LC528" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">    </span>fastq="samples/{sample}.fastq",</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

529

</td>

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

<pre style="margin: 0;">+<span id="LC529" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">    </span>idx=multiext("genome.fa", ".amb", ".ann", ".bwt", ".pac", ".sa")</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

530

</td>

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

<pre style="margin: 0;">+<span id="LC530" class="line" lang="mosel"><span class="s1" style="color: #d14;">    <span class="idiff left right">    </span>conda:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

531

</td>

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

<pre style="margin: 0;">+<span id="LC531" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">    "environment.ya</span>ml"</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

532

</td>

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

<pre style="margin: 0;">+<span id="LC532" class="line" lang="mosel"><span class="s1" style="color: #d14;">    <span class="idiff left right">    </span>output:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

533

</td>

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

<pre style="margin: 0;">+<span id="LC533" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">    </span>"mapped_reads/{sample}.bam"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

534

</td>

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

<pre style="margin: 0;">+<span id="LC534" class="line" lang="mosel"><span class="s1" style="color: #d14;">    <span class="idiff left right">    </span>params:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

535

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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="LC535" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">    </span>idx=lambda w, input: os.path.splitext(input.idx[0])[0]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

536

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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="LC536" class="line" lang="mosel"><span class="s1" style="color: #d14;">    <span class="idiff left right">    </span>shell:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

537

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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="LC537" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">    </span>"bwa mem {params.idx} {input.fastq} | samtools view -Sb - > {output}"</span></span>

</pre>

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512

</td>

<td class="diff-line-num new_line" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

538

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

<pre style="margin: 0;"> <span id="LC538" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

513

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<td class="diff-line-num new_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

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

<pre style="margin: 0;"> <span id="LC539" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

514

</td>

<td class="diff-line-num new_line" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

540

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

<pre style="margin: 0;"> <span id="LC540" class="line" lang="mosel"><span class="s1" style="color: #d14;">to this:</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="517" style="width: 35px; color: rgba(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="543" style="width: 35px; color: rgba(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">@@ -517,14 +543,14 @@ to this:</td>

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<td class="diff-line-num old_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

517

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<td class="diff-line-num new_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

543

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

<pre style="margin: 0;"> <span id="LC543" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

518

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<td class="diff-line-num new_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

544

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

<pre style="margin: 0;"> <span id="LC544" class="line" lang="mosel"><span class="s1" style="color: #d14;">    rule bwa_map:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

519

</td>

<td class="diff-line-num new_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

545

</td>

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

<pre style="margin: 0;"> <span id="LC545" class="line" lang="mosel"><span class="s1" style="color: #d14;">        input:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

520

</td>

<td class="diff-line-num new_line old" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC520" class="line" lang="mosel"><span class="s1" style="color: #d14;">        fastq="samples/{sample}.fastq",</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

521

</td>

<td class="diff-line-num new_line old" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC521" class="line" lang="mosel"><span class="s1" style="color: #d14;">        idx=multiext("genome.fa", ".amb", ".ann", ".bwt", ".pac", ".sa")</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

522

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<td class="diff-line-num new_line old" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC522" class="line" lang="mosel"><span class="s1" style="color: #d14;">    output:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

523

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<pre style="margin: 0;">-<span id="LC523" class="line" lang="mosel"><span class="s1" style="color: #d14;">        "mapped_reads/{sample}.bam"</span></span>

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<pre style="margin: 0;">-<span id="LC524" class="line" lang="mosel"><span class="s1" style="color: #d14;">    params:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC525" class="line" lang="mosel"><span class="s1" style="color: #d14;">        idx=lambda w, input: os.path.splitext(input.idx[0])[0]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC526" class="line" lang="mosel"><span class="s1" style="color: #d14;">    shell:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC527" class="line" lang="mosel"><span class="s1" style="color: #d14;">        "bwa mem {params.idx} {input.fastq} | samtools view -Sb - > {output}"</span></span>

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">    </span>fastq="samples/{sample}.fastq",</span></span>

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">    </span>idx=multiext("genome.fa", ".amb", ".ann", ".bwt", ".pac", ".sa")</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC548" class="line" lang="mosel"><span class="s1" style="color: #d14;">    <span class="idiff left right">    </span>output:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC549" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">    </span>"mapped_reads/{sample}.bam"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC550" class="line" lang="mosel"><span class="s1" style="color: #d14;">    <span class="idiff left right">    </span>params:</span></span>

</pre>

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551

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">    </span>idx=lambda w, input: os.path.splitext(input.idx[0])[0]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC552" class="line" lang="mosel"><span class="s1" style="color: #d14;">    <span class="idiff left right">    </span>shell:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="553" style="width: 35px; color: rgba(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="LC553" class="line" lang="mosel"><span class="s1" style="color: #d14;">        <span class="idiff left right">    </span>"bwa mem {params.idx} {input.fastq} | samtools view -Sb - > {output}"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC554" class="line" lang="mosel"></span>

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<pre style="margin: 0;"> <span id="LC555" class="line" lang="mosel"></span>

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="mosel"><span class="s1" style="color: #d14;">And then for the same command to run everything again, you would need to remove the </span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="870" style="width: 35px; color: rgba(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">@@ -870,16 +896,16 @@ to look like this:</td>

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<pre style="margin: 0;"> <span id="LC896" class="line" lang="mosel"></span>

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<pre style="margin: 0;"> <span id="LC897" class="line" lang="mosel"><span class="s2" style="color: #d14;">    rule bwa_map:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC898" class="line" lang="mosel"><span class="s2" style="color: #d14;">        input:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC873" class="line" lang="mosel"><span class="s2" style="color: #d14;">        fastq="</span><span class="n" style="color: #333;">samples</span><span class="p">/{</span><span class="n" style="color: #333;">sample</span><span class="p">}.</span><span class="n" style="color: #333;">fastq</span><span class="s2" style="color: #d14;">",</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

874

</td>

<td class="diff-line-num new_line old" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC874" class="line" lang="mosel"><span class="s2" style="color: #d14;">        idx=multiext("</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">fa</span><span class="s2" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">amb</span><span class="s2" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">ann</span><span class="s2" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">bwt</span><span class="s2" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">pac</span><span class="s2" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">sa</span><span class="s2" style="color: #d14;">")</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

875

</td>

<td class="diff-line-num new_line old" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC875" class="line" lang="mosel"><span class="s2" style="color: #d14;">    output:</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

876

</td>

<td class="diff-line-num new_line old" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC876" class="line" lang="mosel"><span class="s2" style="color: #d14;">        "</span><span class="n" style="color: #333;">mapped_reads</span><span class="p">/{</span><span class="n" style="color: #333;">sample</span><span class="p">}.</span><span class="n" style="color: #333;">bam</span><span class="s2" style="color: #d14;">"</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

877

</td>

<td class="diff-line-num new_line old" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC877" class="line" lang="mosel"><span class="s2" style="color: #d14;">    params:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

878

</td>

<td class="diff-line-num new_line old" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC878" class="line" lang="mosel"><span class="s2" style="color: #d14;">        idx=lambda w, input: os.path.splitext(input.idx[0])[0]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

879

</td>

<td class="diff-line-num new_line old" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC879" class="line" lang="mosel"><span class="s2" style="color: #d14;">    shell:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

880

</td>

<td class="diff-line-num new_line old" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC880" class="line" lang="mosel"><span class="s2" style="color: #d14;">        "</span><span class="n" style="color: #333;">bwa</span> <span class="n" style="color: #333;">mem</span> <span class="p">{</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">idx</span><span class="p">}</span> <span class="p">{</span><span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">fastq</span><span class="p">}</span> <span class="p">|</span> <span class="n" style="color: #333;">samtools</span> <span class="n" style="color: #333;">view</span> <span class="p">-</span><span class="n" style="color: #333;">Sb</span> <span class="p">-</span> <span class="p">></span> <span class="p">{</span><span class="n" style="color: #333;">output</span><span class="p">}</span><span class="s2" style="color: #d14;">"</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

881

</td>

<td class="diff-line-num new_line old" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC881" class="line" lang="mosel"><span class="s2" style="color: #d14;">    log:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

882

</td>

<td class="diff-line-num new_line old" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC882" class="line" lang="mosel"><span class="s2" style="color: #d14;">        "</span><span class="n" style="color: #333;">logs</span><span class="p">/</span><span class="n" style="color: #333;">bwa_map</span><span class="p">/{</span><span class="n" style="color: #333;">sample</span><span class="p">}.</span><span class="nb" style="color: #0086b3;">log</span><span class="s2" style="color: #d14;">" </span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

899

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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="LC899" class="line" lang="mosel"><span class="s2" style="color: #d14;">        <span class="idiff left right">    </span>fastq="</span><span class="n" style="color: #333;">samples</span><span class="p">/{</span><span class="n" style="color: #333;">sample</span><span class="p">}.</span><span class="n" style="color: #333;">fastq</span><span class="s2" style="color: #d14;">",</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

900

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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="LC900" class="line" lang="mosel"><span class="s2" style="color: #d14;">        <span class="idiff left right">    </span>idx=multiext("</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">fa</span><span class="s2" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">amb</span><span class="s2" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">ann</span><span class="s2" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">bwt</span><span class="s2" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">pac</span><span class="s2" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">sa</span><span class="s2" style="color: #d14;">")</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

901

</td>

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

<pre style="margin: 0;">+<span id="LC901" class="line" lang="mosel"><span class="s2" style="color: #d14;">    <span class="idiff left right">    </span>output:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

902

</td>

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

<pre style="margin: 0;">+<span id="LC902" class="line" lang="mosel"><span class="s2" style="color: #d14;">        <span class="idiff left right">    </span>"</span><span class="n" style="color: #333;">mapped_reads</span><span class="p">/{</span><span class="n" style="color: #333;">sample</span><span class="p">}.</span><span class="n" style="color: #333;">bam</span><span class="s2" style="color: #d14;">"</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

903

</td>

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

<pre style="margin: 0;">+<span id="LC903" class="line" lang="mosel"><span class="s2" style="color: #d14;">    <span class="idiff left right">    </span>params:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

904

</td>

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

<pre style="margin: 0;">+<span id="LC904" class="line" lang="mosel"><span class="s2" style="color: #d14;">        <span class="idiff left right">    </span>idx=lambda w, input: os.path.splitext(input.idx[0])[0]</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

905

</td>

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

<pre style="margin: 0;">+<span id="LC905" class="line" lang="mosel"><span class="s2" style="color: #d14;">    <span class="idiff left right">    </span>shell:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

906

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<pre style="margin: 0;">+<span id="LC906" class="line" lang="mosel"><span class="s2" style="color: #d14;">        <span class="idiff left right">    </span>"</span><span class="n" style="color: #333;">bwa</span> <span class="n" style="color: #333;">mem</span> <span class="p">{</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">idx</span><span class="p">}</span> <span class="p">{</span><span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">fastq</span><span class="p">}</span> <span class="p">|</span> <span class="n" style="color: #333;">samtools</span> <span class="n" style="color: #333;">view</span> <span class="p">-</span><span class="n" style="color: #333;">Sb</span> <span class="p">-</span> <span class="p">></span> <span class="p">{</span><span class="n" style="color: #333;">output</span><span class="p">}</span><span class="s2" style="color: #d14;">"</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

907

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<pre style="margin: 0;">+<span id="LC907" class="line" lang="mosel"><span class="s2" style="color: #d14;">    <span class="idiff left right">    </span>log:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

908

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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="LC908" class="line" lang="mosel"><span class="s2" style="color: #d14;">        <span class="idiff left right">    </span>"</span><span class="n" style="color: #333;">logs</span><span class="p">/</span><span class="n" style="color: #333;">bwa_map</span><span class="p">/{</span><span class="n" style="color: #333;">sample</span><span class="p">}.</span><span class="nb" style="color: #0086b3;">log</span><span class="s2" style="color: #d14;">" </span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

883

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<td class="diff-line-num new_line" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

909

</td>

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

<pre style="margin: 0;"> <span id="LC909" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

884

</td>

<td class="diff-line-num new_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

910

</td>

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

<pre style="margin: 0;"> <span id="LC910" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

885

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<td class="diff-line-num new_line" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

911

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

<pre style="margin: 0;"> <span id="LC911" class="line" lang="mosel"><span class="s2" style="color: #d14;">In the above, we would write a log file to storage in a "</span><span class="n" style="color: #333;">subfolder</span><span class="s2" style="color: #d14;">" of the</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="892" style="width: 35px; color: rgba(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="918" style="width: 35px; color: rgba(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">@@ -892,6 +918,7 @@ good to remember when debugging that:</td>

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892

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<td class="diff-line-num new_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

918

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

<pre style="margin: 0;"> <span id="LC918" class="line" lang="mosel"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

893

</td>

<td class="diff-line-num new_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

919

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<pre style="margin: 0;"> <span id="LC919" class="line" lang="mosel"><span class="s2" style="color: #d14;"> - You should not make assumptions about anything's existence. Use print statements to verify.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

894

</td>

<td class="diff-line-num new_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

920

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<pre style="margin: 0;"> <span id="LC920" class="line" lang="mosel"><span class="s2" style="color: #d14;"> - The biggest errors tend to be syntax and/or path errors</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

921

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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="LC921" class="line" lang="mosel"><span class="s2" style="color: #d14;"> - If you want to test a different snakemake container, you can use the `--container` flag.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

895

</td>

<td class="diff-line-num new_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

922

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<pre style="margin: 0;"> <span id="LC922" class="line" lang="mosel"><span class="s2" style="color: #d14;"> - If the error is especially challenging, set up a small toy example that implements the most basic functionality that you want to achieve.</span></span>

</pre>

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<td class="diff-line-num 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">

896

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<td class="diff-line-num new_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

923

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<pre style="margin: 0;"> <span id="LC923" class="line" lang="mosel"><span class="s2" style="color: #d14;"> - If you need help, reach out to ask for it! If there is an issue with the Google Life Sciences workflow executor, please `open an issue <https://github.com/snakemake/snakemake/issues>`_.</span></span>

</pre>

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897

</td>

<td class="diff-line-num new_line old" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC897" class="line" lang="mosel"><span class="s2" style="color: #d14;"> - It also sometimes helps to take a break from working on somethig, and coming back with fresh eyes.</span></span></pre>

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<td class="diff-line-num new old_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

924

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<pre style="margin: 0;">+<span id="LC924" class="line" lang="mosel"><span class="s2" style="color: #d14;"> - It also sometimes helps to take a break from working on somethi<span class="idiff left right">n</span>g, and coming back with fresh eyes.</span></span></pre>

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<br>

</li>

<li id="cd3fd8615ae98556916b352d1dff137ff81c4027">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#cd3fd8615ae98556916b352d1dff137ff81c4027"><strong>docs/executor_tutorial/tutorial.rst</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,3 +24,7 @@ We ensured that no bioinformatics knowledge is needed to understand the tutorial</td>

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24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">   :maxdepth: 2</span>

</pre>

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25

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>

</pre>

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26

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

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

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">   azure_aks</span>

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

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">   </span></pre>

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<br>

</li>

<li id="d0153cac95479af9bfb99b746b633bc8255bb53a">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#d0153cac95479af9bfb99b746b633bc8255bb53a"><strong>docs/index.rst</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,53 +37,8 @@ Workflows are described via a human readable, Python based language.</td>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition.</span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.</span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">Snakemake is **highly popular** with, `~3 new citations per week <https://badge.dimensions.ai/details/id/pub.1018944052>`_.</span>

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

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">.. _manual-quick_example:</span>

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

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">-------------</span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">Quick Example</span>

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

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

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">Snakemake workflows are essentially Python scripts extended by declarative code to define **rules**.</span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">Rules describe how to create **output files** from **input files**.</span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">.. code-block:: python</span>

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

</td>

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

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

</pre>

</td>

</tr>

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

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

54

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">    rule targets:</span>

</pre>

</td>

</tr>

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

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

55

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">        input:</span>

</pre>

</td>

</tr>

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

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

56

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">            "plots/myplot.pdf"</span>

</pre>

</td>

</tr>

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

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

57

</td>

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

</td>

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

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

</pre>

</td>

</tr>

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

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

58

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">    rule transform:</span>

</pre>

</td>

</tr>

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

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

59

</td>

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

</td>

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

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

</pre>

</td>

</tr>

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

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

60

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">            "raw/{dataset}.csv"</span>

</pre>

</td>

</tr>

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

61

</td>

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

</td>

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

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

</pre>

</td>

</tr>

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

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

62

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">            "transformed/{dataset}.csv"</span>

</pre>

</td>

</tr>

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

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

63

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">        singularity:</span>

</pre>

</td>

</tr>

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

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

64

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">            "docker://somecontainer:v1.0"</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

65

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">        shell:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

66

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">            "somecommand {input} {output}"</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

67

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

68

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">    rule aggregate_and_plot:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

69

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">        input:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

70

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">            expand("transformed/{dataset}.csv", dataset=[1, 2])</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

71

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">        output:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

72

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">            "plots/myplot.pdf"</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

73

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">        conda:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

74

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext">            "envs/matplotlib.yaml"</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

75

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">        script:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">            "scripts/plot.py"</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

77

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">* Similar to GNU Make, you specify targets in terms of a pseudo-rule at the top.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">* For each target and intermediate file, you create rules that define how they are created from input files.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">* Snakemake determines the rule dependencies by matching file names.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">* Input and output files can contain multiple named wildcards.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">* Rules can either use shell commands, plain Python code or external Python or R scripts to create output files from input files.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">* Snakemake workflows can be easily executed on **workstations**, **clusters**, **the grid**, and **in the cloud** without modification. The job scheduling can be constrained by arbitrary resources like e.g. available CPU cores, memory or GPUs.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext">* Snakemake can automatically deploy required software dependencies of a workflow using `Conda <https://conda.io>`_ or `Singularity <https://sylabs.io/docs/>`_.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">* Snakemake can use Amazon S3, Google Storage, Dropbox, FTP, WebDAV, SFTP and iRODS to access input or output files and further access input files via HTTP and HTTPS.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Snakemake is **highly popular** with, `>5 new citations per week <https://badge.dimensions.ai/details/id/pub.1018944052>`_.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">For an introduction, please visit https://snakemake.github.io.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(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="LC43" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">.. _main-getting-started:</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" style="width: 35px; color: rgba(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="47" style="width: 35px; color: rgba(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">@@ -92,10 +47,10 @@ Rules describe how to create **output files** from **input files**.</td>

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="plaintext">Getting started</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">To get a first impression, <span class="idiff left right">see our `introductory slides <https://slides.com/johanneskoester/snakemake-short>`_ or watch the `live demo video <https://youtu.be/hPrXcUUp70Y>`_</span>.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">To get a first impression, <span class="idiff left right">please visit https://snakemake.github.io</span>.</span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">News about Snakemake are published via `Twitter <https://twitter.com/search?l=&q=%23snakemake%20from%3Ajohanneskoester>`_.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(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="LC52" class="line" lang="plaintext">To learn Snakemake, please do the :ref:`tutorial`, and see the :ref:`FAQ <project_info-faq>`.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">For more advanced usage o<span class="idiff left right">f different executor</span>s, see the :ref:`executor_tutorial`.</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">For more advanced usage o<span class="idiff left right">n various platform</span>s, see the :ref:`executor_tutorial`.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">.. _main-support:</span>

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

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

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

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

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="60" style="width: 35px; color: rgba(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">@@ -105,10 +60,10 @@ Support</td>

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

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<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(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="LC60" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(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="LC61" class="line" lang="plaintext">* For releases, see :ref:`Changelog <changelog>`.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(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="LC62" class="line" lang="plaintext">* Check :ref:`frequently asked questions (FAQ) <project_info-faq>`.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext">* In case of <span class="idiff left right">questions</span>, please post on `stack overflow <https://stackoverflow.com/questions/tagged/snakemake>`_.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext">* To <span class="idiff left right">discuss</span> with other Snakemake users, you can use the `mailing list <https://groups.google.com/forum/#!forum/snakemake>`_. **Please do not post questions there. Use stack overflow for questions.**</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">* For <span class="idiff left right">bugs and feature requests</span>, please use the `issue tracker <https://github.com/snakemake/snakemake/issues>`_.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">* For <span class="idiff left right">contributions</span>, visit Snakemake on `Github <https://github.com/snakemake/snakemake>`_ and read the :ref:`guidelines <project_info-contributing>`.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">* In case of <span class="idiff left right">**questions**</span>, please post on `stack overflow <https://stackoverflow.com/questions/tagged/snakemake>`_.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">* To <span class="idiff left right">**discuss**</span> with other Snakemake users, you can use the `mailing list <https://groups.google.com/forum/#!forum/snakemake>`_. **Please do not post questions there. Use stack overflow for questions.**</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">* For <span class="idiff left right">**bugs and feature requests**</span>, please use the `issue tracker <https://github.com/snakemake/snakemake/issues>`_.</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">* For <span class="idiff left right">**contributions**</span>, visit Snakemake on `Github <https://github.com/snakemake/snakemake>`_ and read the :ref:`guidelines <project_info-contributing>`.</span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"></span>

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

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">Citation</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" style="width: 35px; color: rgba(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">@@ -137,62 +92,6 @@ Resources</td>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext">`Bioconda <https://bioconda.github.io/>`_</span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext">    Bioconda can be used from Snakemake for creating completely reproducible workflows by defining the used software versions and providing binaries.</span>

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

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext">.. project_info-publications_using:</span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext">----------------------------</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext">Publications using Snakemake</span>

</pre>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext">----------------------------</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext">In the following you find an **incomplete list** of publications making use of Snakemake for their analyses.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext">Please consider to add your own.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext">* Rubert et al. 2020. _`Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants <https://doi.org/10.1186/s12864-020-6609-x>`_. BMC Genomics.</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="plaintext">* Kuzniar et al. 2020. `sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data <https://doi.org/10.7717/peerj.8214>`_. PeerJ.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext">* Doris et al. 2018. `Spt6 is required for the fidelity of promoter selection <https://doi.org/10.1016/j.molcel.2018.09.005>`_. Molecular Cell.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext">* Karlsson et al. 2018. `Four evolutionary trajectories underlie genetic intratumoral variation in childhood cancer <https://www.nature.com/articles/s41588-018-0131-y>`_. Nature Genetics.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC191" class="line" lang="plaintext">* Martin et al. 2013. `Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3 <https://www.nature.com/ng/journal/v45/n8/full/ng.2674.html>`_. Nature Genetics.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC192" class="line" lang="plaintext">* Czeschik et al. 2013. `Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome <https://link.springer.com/article/10.1007%2Fs00439-013-1295-2>`_. Human Genetics.</span>

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="plaintext">* Marschall et al. 2012. `CLEVER: Clique-Enumerating Variant Finder <https://bioinformatics.oxfordjournals.org/content/28/22/2875.long>`_. Bioinformatics.</span>

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC195" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">.. toctree::</span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext">   :caption: Getting started</span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">   :name: getting_started</span>

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<br>

</li>

<li id="4d96bc0560e0c9e4668ccb39b500cece62a72820">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#4d96bc0560e0c9e4668ccb39b500cece62a72820"><strong>docs/project_info/authors.rst</strong></a>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +21,7 @@ Development Team</td>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">- Wibowo Arindrarto</span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">- Rasmus Ågren</span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">- Soohyun Lee</span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">- Vanessa Sochat</span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>

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

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">------------</span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,4 +58,5 @@ In alphabetical order</td>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">- Sean Davis</span>

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

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">- Tobias Marschall</span>

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

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">- Vanessa Sochat</span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">- Willem Ligtenberg</span></pre>

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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#945ec74fc1c17902d98bca84b7a1f0dfd755c01b"><strong>docs/snakefiles/deployment.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">@@ -222,10 +222,10 @@ Snakemake allows to define environment modules per rule:</td>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="plaintext">        shell:</span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="plaintext">            "bwa mem {input} | samtools view -Sbh - > {output}"</span>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="plaintext">Here, when Snakemake is executed with `<span class="idiff left right">snakemake --use-envmodules</span>`, it will load the defined modules in the given order, instead of using the also defined conda environment.</span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">Here, when Snakemake is executed with `<span class="idiff left right">`snakemake --use-envmodules`</span>`, it will load the defined modules in the given order, instead of using the also defined conda environment.</span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="plaintext">Note that although not mandatory, one should always provide either a conda environment or a container (see above), along with environment module definitions.</span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="plaintext">The reason is that environment modules are often highly platform specific, and cannot be assumed to be available somewhere else, thereby limiting reproducibility.</span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="plaintext">By definition an equivalent conda environment or container as a fallback, people outside of the HPC system where the workflow has been designed can still execute it, e.g. by running `<span class="idiff left right">snakemake --use-conda` instead of `snakemake --use-envmodules</span>`.</span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">By definition an equivalent conda environment or container as a fallback, people outside of the HPC system where the workflow has been designed can still execute it, e.g. by running `<span class="idiff left right">`snakemake --use-conda`` instead of ``snakemake --use-envmodules`</span>`.</span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="plaintext">--------------------------------------</span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="plaintext">Sustainable and reproducible archiving</span>

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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#678d7e50121966ef613372bf85b3e7f144e00ef1"><strong>docs/snakefiles/remote_files.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">@@ -14,7 +14,7 @@ Snakemake includes the following remote providers, supported by the correspondin</td>

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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">* Amazon Simple Storage Service (AWS S3): ``snakemake.remote.S3``</span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">* Google Cloud Storage (GS): ``snakemake.remote.GS``</span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">* Microsoft Azure <span class="idiff left right">Storage: ``snakemake.remote.AzureStorage</span>``</span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">* Microsoft Azure <span class="idiff left right">Blob Storage: ``snakemake.remote.AzBlob</span>``</span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">* File transfer over SSH (SFTP): ``snakemake.remote.SFTP``</span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">* Read-only web (HTTP[S]): ``snakemake.remote.HTTP``</span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">* File transfer protocol (FTP): ``snakemake.remote.FTP``</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">@@ -139,28 +139,37 @@ In the Snakefile, no additional authentication information has to be provided:</td>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext">            GS.remote("bucket-name/file.txt")</span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext">Microsoft Azure Storage</span>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext">=======================</span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">Microsoft Azure Blob Storage</span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">=============================</span>

</pre>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">Usage of the Azure Blob Storage provider is similar to the S3 provider. For</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(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="LC146" class="line" lang="plaintext">authentication, an account name and shared access signature (SAS) or key can be used. If these</span>

</pre>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">variables are not passed directly to AzureRemoteProvider (see</span>

</pre>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">[BlobServiceClient</span>

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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(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="LC149" class="line" lang="plaintext">class](https://docs.microsoft.com/en-us/python/api/azure-storage-blob/azure.storage.blob.blobserviceclient?view=azure-python)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(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="LC150" class="line" lang="plaintext">for naming), they will be read from environment variables, named</span>

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

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">`AZ_BLOB_ACCOUNT_URL` and `AZ_BLOB_CREDENTIAL`. `AZ_BLOB_ACCOUNT_URL` takes the form</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(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="LC152" class="line" lang="plaintext">`https://<accountname>.blob.core.windows.net` and may also contain a SAS. If</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(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="LC153" class="line" lang="plaintext">a SAS is not part of the URL, `AZ_BLOB_CREDENTIAL` has to be set to the SAS or alternatively to</span>

</pre>

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">the storage account key.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext"><span class="idiff left right">Usage of the Azure Storage provider is similar to the S3 provider.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext"><span class="idiff left right">For authentication, one needs to provide an account name and a key</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext"><span class="idiff left right">or SAS token (without leading question mark), which can for example</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext"><span class="idiff left right">be read from environment variables</span>.</span>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(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="LC156" class="line" lang="plaintext"><span class="idiff left right">When using AzBlob as default remote provider you will almost always want to</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"><span class="idiff left right">pass these environment variables on to the remote execution environment (e.g.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"><span class="idiff left right">Kubernetes) with `--envvars`, e.g</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"><span class="idiff left right">`--envvars AZ_BLOB_ACCOUNT_URL AZ_BLOB_CREDENTIAL`</span>.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext">.. code-block:: python</span>

</pre>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext">    from snakemake.remote.AzureStorage import RemoteProvider as AzureRemoteProvider</span>

</pre>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext">    account_name=os.environ['AZURE_ACCOUNT']</span>

</pre>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext">    account_key=os.environ.get('AZURE_KEY')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext">    sas_token=os.environ.get('SAS_TOKEN')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="plaintext">    assert account_key or sas_token</span>

</pre>

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="plaintext">    AS = AzureRemoteProvider(account_name=account_name, account_key=account_key, sas_token=sas_token)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">    from snakemake.remote.AzBlob import RemoteProvider as AzureRemoteProvider</span>

</pre>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">    AS = AzureRemoteProvider()# assumes env vars AZ_BLOB_ACCOUNT_URL and possibly AZ_BLOB_CREDENTIAL are set</span>

</pre>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext">    rule a:</span>

</pre>

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

160

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext">        input:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

161

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext">            AS.remote("path/to/file.txt")</span>

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162

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169

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext"></span>

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163

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170

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(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="LC171" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="164" style="width: 35px; color: rgba(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="LC172" class="line" lang="plaintext"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="plaintext">File transfer over SSH (SFTP)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="plaintext">=============================</span>

</pre>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="plaintext"></span>

</pre>

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<br>

</li>

<li id="f2ad3e3ae7fe1cf3ff9f5d75e080faf74d1d8980">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#f2ad3e3ae7fe1cf3ff9f5d75e080faf74d1d8980"><strong>docs/snakefiles/reporting.rst</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -100,8 +100,8 @@ You can define an institute specific stylesheet with:</td>

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

</pre>

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

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">In particular, this allows you to e.g. set a logo at the top (by using CSS to inject a background for the placeholder ``<div id="brand">``, or overwrite colors.</span>

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

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">For an example custom stylesheet defining the logo, see :download:`here <../../tests/test_report/custom-stylesheet.css>`.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext">The report for above example can be found :download:`here <../../tests/test_report/report.html>` (with a custom branding for the University of Duisburg-Essen).</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext">The full example source code can be found `here <https://github.com/snakemake/snakemake/<span class="idiff left right">src</span>/master/tests/test_report/>`_.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">The report for above example can be found :download:`here <../../tests/test_report/<span class="idiff left right">expected-results/</span>report.html>` (with a custom branding for the University of Duisburg-Essen).</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">The full example source code can be found `here <https://github.com/snakemake/snakemake/<span class="idiff left right">tree</span>/master/tests/test_report/>`_.</span>

</pre>

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

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(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="LC106" class="line" lang="plaintext">Note that the report can be restricted to particular jobs and results by specifying targets at the command line, analog to normal Snakemake execution.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext">For example, with</span>

</pre>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(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="72" style="width: 35px; color: rgba(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">@@ -72,8 +72,8 @@ setup(</td>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python">        <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 class="s" style="color: #d14;">"pygments"</span><span class="p">,</span> <span class="s" style="color: #d14;">"pygraphviz"</span><span class="p">],</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python">        <span class="s" style="color: #d14;">"messaging"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"slacker"</span><span class="p">],</span></span>

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

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python">        <span class="s" style="color: #d14;">"google-cloud"</span><span class="p">:</span> <span class="p">[</span></span>

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<td class="diff-line-num new_line old" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python">            <span class="s" style="color: #d14;">"crc32c"</span><span class="p">,</span></span>

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

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python">            <span class="s" style="color: #d14;">"oauth2client"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python">            <span class="s" style="color: #d14;">"google-crc32c"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="77" style="width: 35px; color: rgba(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="LC77" class="line" lang="python">            <span class="s" style="color: #d14;">"google-api-python-client"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python">            <span class="s" style="color: #d14;">"google-cloud-storage"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python">        <span class="p">],</span></span>

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</li>

<li id="d366205d7cd679ff6d4a61f70728e92537101763">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#d366205d7cd679ff6d4a61f70728e92537101763"><strong>snakemake/__init__.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="444" style="width: 35px; color: rgba(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="444" style="width: 35px; color: rgba(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">@@ -444,7 +444,8 @@ def snakemake(</td>

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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cluster_mode</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="LC445" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: cluster and drmaa args are mutually exclusive"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">debug</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">cluster_mode</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="448" style="width: 35px; color: rgba(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="LC447" class="line" lang="python"></span>

</pre>

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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;">debug</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">cluster_mode</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">cores</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="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

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448

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<td class="diff-line-num new_line" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

449

</td>

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

<pre style="margin: 0;"> <span id="LC449" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

449

</td>

<td class="diff-line-num new_line" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

450

</td>

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

<pre style="margin: 0;"> <span id="LC450" class="line" lang="python">            <span class="s" style="color: #d14;">"Error: debug mode cannot be used with more than one core or cluster execution."</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

450

</td>

<td class="diff-line-num new_line" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

451

</td>

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

<pre style="margin: 0;"> <span id="LC451" class="line" lang="python">        <span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1533" style="width: 35px; color: rgba(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="1534" style="width: 35px; color: rgba(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">@@ -1533,6 +1534,7 @@ def get_argument_parser(profile=None):</td>

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<td class="diff-line-num old_line" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1533

</td>

<td class="diff-line-num new_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1534

</td>

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

<pre style="margin: 0;"> <span id="LC1534" class="line" lang="python">        <span class="s" style="color: #d14;">"fractions allowed."</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1534

</td>

<td class="diff-line-num new_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1535

</td>

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

<pre style="margin: 0;"> <span id="LC1535" class="line" lang="python">    <span class="p">)</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1535

</td>

<td class="diff-line-num new_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1536

</td>

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

<pre style="margin: 0;"> <span id="LC1536" class="line" lang="python">    <span class="n" style="color: #333;">group_behavior</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1537

</td>

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

<pre style="margin: 0;">+<span id="LC1537" class="line" lang="python">        <span class="s" style="color: #d14;">"-T"</span><span class="p">,</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1536

</td>

<td class="diff-line-num new_line" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1538

</td>

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

<pre style="margin: 0;"> <span id="LC1538" class="line" lang="python">        <span class="s" style="color: #d14;">"--restart-times"</span><span class="p">,</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1537

</td>

<td class="diff-line-num new_line" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1539

</td>

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

<pre style="margin: 0;"> <span id="LC1539" class="line" lang="python">        <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1538

</td>

<td class="diff-line-num new_line" data-linenumber="1540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1540

</td>

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

<pre style="margin: 0;"> <span id="LC1540" class="line" lang="python">        <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1557" style="width: 35px; color: rgba(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">@@ -1555,7 +1557,17 @@ def get_argument_parser(profile=None):</td>

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<td class="diff-line-num old_line" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1555

</td>

<td class="diff-line-num new_line" data-linenumber="1557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1557

</td>

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

<pre style="margin: 0;"> <span id="LC1557" class="line" lang="python">    <span class="p">)</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1556

</td>

<td class="diff-line-num new_line" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1558

</td>

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

<pre style="margin: 0;"> <span id="LC1558" class="line" lang="python">    <span class="n" style="color: #333;">group_behavior</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1557

</td>

<td class="diff-line-num new_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1559

</td>

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

<pre style="margin: 0;"> <span id="LC1559" class="line" lang="python">        <span class="s" style="color: #d14;">"--default-remote-provider"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1558

</td>

<td class="diff-line-num new_line old" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1558" class="line" lang="python">        <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"S3"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GS"</span><span class="p">,</span> <span class="s" style="color: #d14;">"FTP"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SFTP"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S3Mocked"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gfal"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gridftp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"iRODS"</span><span class="p">],</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1560

</td>

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

<pre style="margin: 0;">+<span id="LC1560" class="line" lang="python">        <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1561

</td>

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

<pre style="margin: 0;">+<span id="LC1561" class="line" lang="python">            <span class="s" style="color: #d14;">"S3"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1562

</td>

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

<pre style="margin: 0;">+<span id="LC1562" class="line" lang="python">            <span class="s" style="color: #d14;">"GS"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1563

</td>

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

<pre style="margin: 0;">+<span id="LC1563" class="line" lang="python">            <span class="s" style="color: #d14;">"FTP"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1564

</td>

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

<pre style="margin: 0;">+<span id="LC1564" class="line" lang="python">            <span class="s" style="color: #d14;">"SFTP"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1565

</td>

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

<pre style="margin: 0;">+<span id="LC1565" class="line" lang="python">            <span class="s" style="color: #d14;">"S3Mocked"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1566

</td>

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

<pre style="margin: 0;">+<span id="LC1566" class="line" lang="python">            <span class="s" style="color: #d14;">"gfal"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1567

</td>

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

<pre style="margin: 0;">+<span id="LC1567" class="line" lang="python">            <span class="s" style="color: #d14;">"gridftp"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1568

</td>

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

<pre style="margin: 0;">+<span id="LC1568" class="line" lang="python">            <span class="s" style="color: #d14;">"iRODS"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1569

</td>

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

<pre style="margin: 0;">+<span id="LC1569" class="line" lang="python">            <span class="s" style="color: #d14;">"AzBlob"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1570

</td>

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

<pre style="margin: 0;">+<span id="LC1570" class="line" lang="python">        <span class="p">],</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1559

</td>

<td class="diff-line-num new_line" data-linenumber="1571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1571

</td>

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

<pre style="margin: 0;"> <span id="LC1571" class="line" lang="python">        <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Specify default remote provider to be used for "</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1560

</td>

<td class="diff-line-num new_line" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1572

</td>

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

<pre style="margin: 0;"> <span id="LC1572" class="line" lang="python">        <span class="s" style="color: #d14;">"all input and output files that don't yet specify "</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1561

</td>

<td class="diff-line-num new_line" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1573

</td>

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

<pre style="margin: 0;"> <span id="LC1573" class="line" lang="python">        <span class="s" style="color: #d14;">"one."</span><span class="p">,</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="5e16cbeea010f59dbef52f8950f4873c94f39c7e">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#5e16cbeea010f59dbef52f8950f4873c94f39c7e"><strong>snakemake/_version.py</strong></a>

<hr>

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

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,9 +22,9 @@ def get_keywords():</td>

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

22

</td>

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

22

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

<pre style="margin: 0;"> <span id="LC22" 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>

</pre>

</td>

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

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

23

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

23

</td>

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

<pre style="margin: 0;"> <span id="LC23" 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>

</pre>

</td>

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

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

24

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

24

</td>

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

<pre style="margin: 0;"> <span id="LC24" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># get_keywords().</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC25" 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: v5.20</span>.1)"</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

</td>

<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC26" class="line" lang="python">    <span 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">7dd7d8b1cad48f9369deb42b54be3d52fcd65dd9</span>"</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

</td>

<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC27" 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;">"2020-0<span class="idiff left right">7-09 11:13:42</span> +0200"</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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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="LC25" 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: v5.22</span>.1)"</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

</td>

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

<pre style="margin: 0;">+<span id="LC26" 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">982f1d1f5bb55eda1caa8f15853041922ef4bea0</span>"</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC27" 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;">"2020-0<span class="idiff left right">8-14 08:41:41</span> +0200"</span></span>

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<pre style="margin: 0;"> <span id="LC28" 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="LC29" 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="LC30" class="line" lang="python"></span>

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<li id="7610d24f21cc1508e60687b4a0c7e940a75ca358">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#7610d24f21cc1508e60687b4a0c7e940a75ca358"><strong>snakemake/executors/__init__.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1363" style="width: 35px; color: rgba(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="1363" style="width: 35px; color: rgba(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">@@ -1363,7 +1363,7 @@ class KubernetesExecutor(ClusterExecutor):</td>

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<pre style="margin: 0;"> <span id="LC1363" class="line" lang="python">            <span class="s" style="color: #d14;">"cp -rf /source/. . && "</span></span>

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<pre style="margin: 0;"> <span id="LC1364" class="line" lang="python">            <span class="s" style="color: #d14;">"snakemake {target} --snakefile {snakefile} "</span></span>

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<pre style="margin: 0;"> <span id="LC1365" class="line" lang="python">            <span class="s" style="color: #d14;">"--force -j{cores} --keep-target-files  --keep-remote "</span></span>

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<pre style="margin: 0;">-<span id="LC1366" class="line" lang="python">            <span class="s" style="color: #d14;">"--latency-wait <span class="idiff left right">0</span> "</span></span>

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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="python">            <span class="s" style="color: #d14;">"--latency-wait <span class="idiff left right">{latency_wait}</span> "</span></span>

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<pre style="margin: 0;"> <span id="LC1367" class="line" lang="python">            <span class="s" style="color: #d14;">" --attempt {attempt} {use_threads} "</span></span>

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<pre style="margin: 0;"> <span id="LC1368" class="line" lang="python">            <span class="s" style="color: #d14;">"--wrapper-prefix {workflow.wrapper_prefix} "</span></span>

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<pre style="margin: 0;"> <span id="LC1369" class="line" lang="python">            <span class="s" style="color: #d14;">"{overwrite_config} {printshellcmds} {rules} --nocolor "</span></span>

</pre>

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<li id="09eebb28d24925c2b41cf2365dd083ada597795e">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#09eebb28d24925c2b41cf2365dd083ada597795e"><strong>snakemake/executors/google_lifesciences.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,6 +3,7 @@ __copyright__ = "Copyright 2015-2020, Johannes Köster"</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__email__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"koester@jimmy.harvard.edu"</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__license__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"MIT"</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

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<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="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +22,8 @@ from snakemake.exceptions import WorkflowError</td>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.executors</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ClusterExecutor</span><span class="p">,</span> <span class="n" style="color: #333;">sleep</span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.common</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_container_image</span><span class="p">,</span> <span class="n" style="color: #333;">get_file_hash</span></span>

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

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># https://github.com/googleapis/google-api-python-client/issues/299#issuecomment-343255309</span></span>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="s" style="color: #d14;">"googleapiclient.discovery_cache"</span><span class="p">).</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">ERROR</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">GoogleLifeSciencesJob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">namedtuple</span><span class="p">(</span></span>

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">    <span class="s" style="color: #d14;">"GoogleLifeSciencesJob"</span><span class="p">,</span> <span class="s" style="color: #d14;">"job jobname jobid callback error_callback"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" style="width: 35px; color: rgba(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="147" style="width: 35px; color: rgba(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">@@ -144,9 +147,15 @@ class GoogleLifeSciencesExecutor(ClusterExecutor):</td>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ex</span></span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Discovery clients for Google Cloud Storage and Life Sciences API</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_storage_cli</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">discovery_build</span><span class="p">(</span><span class="s" style="color: #d14;">"storage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"v1"</span><span class="p">,</span> <span class="n" style="color: #333;">credentials</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">creds</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_compute_cli</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">discovery_build</span><span class="p">(</span><span class="s" style="color: #d14;">"compute"</span><span class="p">,</span> <span class="s" style="color: #d14;">"v1"</span><span class="p">,</span> <span class="n" style="color: #333;">credentials</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">creds</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_api</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">discovery_build</span><span class="p">(</span><span class="s" style="color: #d14;">"lifesciences"</span><span class="p">,</span> <span class="s" style="color: #d14;">"v2beta"</span><span class="p">,</span> <span class="n" style="color: #333;">credentials</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">creds</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" style="width: 35px; color: rgba(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="LC150" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_storage_cli</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">discovery_build</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python">            <span class="s" style="color: #d14;">"storage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"v1"</span><span class="p">,</span> <span class="n" style="color: #333;">credentials</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">creds</span><span class="p">,</span> <span class="n" style="color: #333;">cache_discovery</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

152

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python">        <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

153

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_compute_cli</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">discovery_build</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(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="LC154" class="line" lang="python">            <span class="s" style="color: #d14;">"compute"</span><span class="p">,</span> <span class="s" style="color: #d14;">"v1"</span><span class="p">,</span> <span class="n" style="color: #333;">credentials</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">creds</span><span class="p">,</span> <span class="n" style="color: #333;">cache_discovery</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

155

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python">        <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

156

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_api</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">discovery_build</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

157

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python">            <span class="s" style="color: #d14;">"lifesciences"</span><span class="p">,</span> <span class="s" style="color: #d14;">"v2beta"</span><span class="p">,</span> <span class="n" style="color: #333;">credentials</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">creds</span><span class="p">,</span> <span class="n" style="color: #333;">cache_discovery</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

158

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python">        <span class="p">)</span></span>

</pre>

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

159

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_bucket_service</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">storage</span><span class="p">.</span><span class="n" style="color: #333;">Client</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

151

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

160

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

161

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_bucket</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="641" style="width: 35px; color: rgba(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="650" style="width: 35px; color: rgba(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">@@ -641,7 +650,7 @@ class GoogleLifeSciencesExecutor(ClusterExecutor):</td>

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<td class="diff-line-num old_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

641

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<td class="diff-line-num new_line" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

650

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<pre style="margin: 0;"> <span id="LC650" class="line" lang="python">        <span class="n" style="color: #333;">commands</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

642

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<td class="diff-line-num new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

651

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python">            <span class="s" style="color: #d14;">"/bin/bash"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

643

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<td class="diff-line-num new_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

652

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="python">            <span class="s" style="color: #d14;">"-c"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

644

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<td class="diff-line-num new_line old" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC644" class="line" lang="python">            <span class="s" style="color: #d14;">"mkdir -p /workdir && cd /workdir && wget -O /download.py https://gist.githubusercontent.com/vsoch/84886ef6469bedeeb9a79a4eb7aec0d1/raw/181499f8f17163dcb2f89822079938cbfbd258cc/download.py && chmod +x /download.py && source activate snakemake || true && p<span class="idiff left right">ip install crc32c && p</span>ython /download.py download %s %s /tmp/workdir.tar.gz && tar -xzvf /tmp/workdir.tar.gz && %s"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

653

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<pre style="margin: 0;">+<span id="LC653" class="line" lang="python">            <span class="s" style="color: #d14;">"mkdir -p /workdir && cd /workdir && wget -O /download.py https://gist.githubusercontent.com/vsoch/84886ef6469bedeeb9a79a4eb7aec0d1/raw/181499f8f17163dcb2f89822079938cbfbd258cc/download.py && chmod +x /download.py && source activate snakemake || true && python /download.py download %s %s /tmp/workdir.tar.gz && tar -xzvf /tmp/workdir.tar.gz && %s"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC654" class="line" lang="python">            <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">bucket</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pipeline_package</span><span class="p">,</span> <span class="n" style="color: #333;">exec_job</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC655" class="line" lang="python">        <span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC656" class="line" lang="python"></span>

</pre>

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<br>

</li>

<li id="93a82c4f9627ca07fc8ef809981ab851baae987e">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#93a82c4f9627ca07fc8ef809981ab851baae987e"><strong>snakemake/remote/AzureStorage.py</strong>

→

<strong>snakemake/remote/AzBlob.py</strong>

</a>

<hr>

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

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

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="s" style="color: #d14;">"""Azure Blob Storage handling</span></span>

</pre>

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

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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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>

</pre>

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1

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

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Sebastian Kurscheid"</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__copyright__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Copyright 2019, Sebastian Kurscheid"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">__email__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"sebastian.kurscheid@anu.edu.au"</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,12 +9,9 @@ __license__ = "MIT"</td>

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

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># built-ins</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">math</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">functools</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">concurrent.futures</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># snakemake specific</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">from</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">snakemake.common</span></span><span class="idiff"> </span><span class="kn" style="font-weight: 600;"><span class="idiff">import</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">lazy_property</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># /</span></span></span>

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

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

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

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># module specific</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">,</span> <span class="n" style="color: #333;">AzureFileException</span></span>

</pre>

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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>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,12 +19,11 @@ from snakemake.remote import AbstractRemoteObject, AbstractRemoteProvider</td>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># service provider support</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">azure.storage.common.cloudstorageaccount</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python">        <span class="n" style="color: #333;">CloudStorageAccount</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">AzureStorageAccount</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python">    <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(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="LC22" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">azure.storage.blob</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BlobServiceClient</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">    <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">azure.core.exceptions</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python">    <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC27" class="line" lang="python">        <span class="s" style="color: #d14;">"The Python 3 package<span class="idiff left right">s 'azure-storage' and 'azure-storage-common</span>' "</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">        <span class="s" style="color: #d14;">"The Python 3 package<span class="idiff left right"> 'azure-storage-blob</span>' "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC27" class="line" lang="python">        <span class="s" style="color: #d14;">"need to be installed to use Azure Storage remote() file functionality. %s"</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">        <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">msg</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">    <span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,26 +75,25 @@ class RemoteObject(AbstractRemoteObject):</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">exists</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="LC76" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_matched_as_path</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_as</span><span class="p">.</span><span class="n" style="color: #333;">exists_in_container</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob_name</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC79" 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="LC80" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">AzureFileException</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python">                <span class="s" style="color: #d14;">"The file cannot be parsed as an Azure Blob path in form 'container/blob': %s"</span></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python">                <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_file</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python">            <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">AzureFileException</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">            <span class="s" style="color: #d14;">"The file cannot be parsed as an Azure Blob path in form 'container/blob': %s"</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">            <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_file</span><span class="p">()</span></span>

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

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mtime</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="LC84" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">():</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># b = self.blob_service_client.get_blob_client(self.container_name, self.blob_name)</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># return b.get_blob_properties().last_modified</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python">            <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_as</span><span class="p">.</span><span class="n" style="color: #333;">blob_last_modified</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob_name</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">t</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">AzureFileException</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python">                <span class="s" style="color: #d14;">"The file does not seem to exist remotely: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_file</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python">            <span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(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="LC89" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">AzureFileException</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(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="LC90" class="line" lang="python">            <span class="s" style="color: #d14;">"The file does not seem to exist remotely: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_file</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(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="LC91" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">size</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">():</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_as</span><span class="p">.</span><span class="n" style="color: #333;">blob_size</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob_name</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_iofile</span><span class="p">.</span><span class="n" style="color: #333;">size_local</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(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="LC96" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_iofile</span><span class="p">.</span><span class="n" style="color: #333;">size_local</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"></span>

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

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">download</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="142" style="width: 35px; color: rgba(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="140" style="width: 35px; color: rgba(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">@@ -142,6 +140,7 @@ class RemoteObject(AbstractRemoteObject):</td>

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<td class="diff-line-num new_line" data-linenumber="140" style="width: 35px; color: rgba(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="LC140" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(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="LC141" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="142" style="width: 35px; color: rgba(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="LC142" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">container_name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<td class="diff-line-num new old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(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="LC143" class="line" lang="python">        <span class="s" style="color: #d14;">"return container name component of the path"</span></span>

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<td class="diff-line-num old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(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="LC144" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_matched_as_path</span><span class="p">.</span><span class="n" style="color: #333;">groups</span><span class="p">())</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(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="LC145" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_matched_as_path</span><span class="p">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="s" style="color: #d14;">"container_name"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="147" style="width: 35px; color: rgba(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="LC146" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</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="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="151" style="width: 35px; color: rgba(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">@@ -152,8 +151,10 @@ class RemoteObject(AbstractRemoteObject):</td>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"></span>

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

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">blob_name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(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="LC154" class="line" lang="python">        <span class="s" style="color: #d14;">"return the blob name component of the path"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="155" style="width: 35px; color: rgba(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="LC155" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_matched_as_path</span><span class="p">.</span><span class="n" style="color: #333;">groups</span><span class="p">())</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_matched_as_path</span><span class="p">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="s" style="color: #d14;">"blob_name"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(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="LC157" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Actual Azure specific functions, adapted from S3.py</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="165" style="width: 35px; color: rgba(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">@@ -164,14 +165,29 @@ class AzureStorageHelper(object):</td>

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<td class="diff-line-num new_line" data-linenumber="165" style="width: 35px; color: rgba(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="LC165" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"stay_on_remote"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python">            <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"stay_on_remote"</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">azure</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AzureStorageAccount</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">).</span><span class="n" style="color: #333;">create_block_blob_service</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if not handed down explicitely, try to read credentials from</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># environment variables.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">csavar</span><span class="p">,</span> <span class="n" style="color: #333;">envvar</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(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="LC171" class="line" lang="python">            <span class="p">(</span><span class="s" style="color: #d14;">"account_url"</span><span class="p">,</span> <span class="s" style="color: #d14;">"AZ_BLOB_ACCOUNT_URL"</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(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="LC172" class="line" lang="python">            <span class="p">(</span><span class="s" style="color: #d14;">"credential"</span><span class="p">,</span> <span class="s" style="color: #d14;">"AZ_BLOB_CREDENTIAL"</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python">        <span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">csavar</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;">kwargs</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">envvar</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">environ</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python">                <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="n" style="color: #333;">csavar</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">environ</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">envvar</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python">            <span class="s" style="color: #d14;">"account_url"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(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="LC178" class="line" lang="python">        <span class="p">),</span> <span class="s" style="color: #d14;">"Missing AZ_BLOB_ACCOUNT_URL env var (and possibly AZ_BLOB_CREDENTIAL)"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># remove leading '?' from SAS if needed</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if kwargs.get("sas_token", "").startswith("?"):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#    kwargs["sas_token"] = kwargs["sas_token"][1:]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># by right only account_key or sas_token should be set, but we let</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(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="LC184" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># BlobServiceClient deal with the ambiguity</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(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="LC185" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob_service_client</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BlobServiceClient</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">container_exists</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">container_name</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC170" 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 old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">azure</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">container_name</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python">            <span class="bp" style="color: #999;">True</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob_service_client</span><span class="p">.</span><span class="n" style="color: #333;">list_containers</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">upload_to_azure_storage</span><span class="p">(</span></span>

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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="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="201" style="width: 35px; color: rgba(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">@@ -201,8 +217,12 @@ class AzureStorageHelper(object):</td>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python">            <span class="s" style="color: #d14;">"The file path specified does not appear to be a file: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">file_path</span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">azure</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">azure</span><span class="p">.</span><span class="n" style="color: #333;">create_container</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">container_name</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python">        <span class="n" style="color: #333;">container_client</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob_service_client</span><span class="p">.</span><span class="n" style="color: #333;">get_container_client</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="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">

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<td class="diff-line-num new new_line" data-linenumber="222" style="width: 35px; color: rgba(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="LC222" class="line" lang="python">            <span class="n" style="color: #333;">container_client</span><span class="p">.</span><span class="n" style="color: #333;">create_container</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(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="LC223" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">azure</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">exceptions</span><span class="p">.</span><span class="n" style="color: #333;">ResourceExistsError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="224" style="width: 35px; color: rgba(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="LC224" class="line" lang="python">            <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="225" style="width: 35px; color: rgba(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="LC225" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC226" 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;">blob_name</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="207" style="width: 35px; color: rgba(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="LC227" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_relative_path_for_blob_name</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">relative_start_dir</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" style="width: 35px; color: rgba(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="232" style="width: 35px; color: rgba(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">@@ -212,14 +232,17 @@ class AzureStorageHelper(object):</td>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python">                <span class="n" style="color: #333;">path_blob_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python">            <span class="n" style="color: #333;">blob_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path_blob_name</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python">        <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">azure</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="235" style="width: 35px; color: rgba(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="LC235" class="line" lang="python">        <span class="n" style="color: #333;">blob_client</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">container_client</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_client</span><span class="p">(</span><span class="n" style="color: #333;">blob_name</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="236" style="width: 35px; color: rgba(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="LC236" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># upload_blob fails, if blob exists</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="238" style="width: 35px; color: rgba(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="LC238" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">exists_in_container</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="239" style="width: 35px; color: rgba(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="LC239" class="line" lang="python">            <span class="n" style="color: #333;">blob_client</span><span class="p">.</span><span class="n" style="color: #333;">delete_blob</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python">            <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">create_blob_from_path</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python">                <span class="n" style="color: #333;">container_name</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;">file_path</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">blob_name</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python">            <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_properties</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">blob_name</span><span class="p">).</span><span class="n" style="color: #333;">name</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC222" 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;">"Error in creating blob. %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="241" style="width: 35px; color: rgba(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="LC241" 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;">file_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">data</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="242" style="width: 35px; color: rgba(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="LC242" class="line" lang="python">                <span class="n" style="color: #333;">blob_client</span><span class="p">.</span><span class="n" style="color: #333;">upload_blob</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">blob_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"BlockBlob"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="243" style="width: 35px; color: rgba(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="LC243" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">blob_client</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_properties</span><span class="p">().</span><span class="n" style="color: #333;">name</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="244" style="width: 35px; color: rgba(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="LC244" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="245" style="width: 35px; color: rgba(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="LC245" 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;">"Error in creating blob. %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># return None</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">download_from_azure_storage</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">@@ -260,24 +283,19 @@ class AzureStorageHelper(object):</td>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if the destination path does not exist</span></span>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">make_dest_dirs</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;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">destination_path</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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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python">        <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">azure</span></span>

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<pre style="margin: 0;">-<span id="LC264" 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 old old_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC265" 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;">create_stub_only</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python">                <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_to_path</span><span class="p">(</span></span>

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<td class="diff-line-num old old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python">                    <span class="n" style="color: #333;">container_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">container_name</span><span class="p">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python">                    <span class="n" style="color: #333;">blob_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">blob_name</span><span class="p">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python">                    <span class="n" style="color: #333;">file_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">destination_path</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;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob_service_client</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_client</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="270" style="width: 35px; color: rgba(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="LC287" 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;">create_stub_only</span><span class="p">:</span></span>

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<td class="diff-line-num new old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(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="LC288" 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;">destination_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">my_blob</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python">                <span class="n" style="color: #333;">blob_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">download_blob</span><span class="p">()</span></span>

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<td class="diff-line-num new old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(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="LC290" class="line" lang="python">                <span class="n" style="color: #333;">blob_data</span><span class="p">.</span><span class="n" style="color: #333;">readinto</span><span class="p">(</span><span class="n" style="color: #333;">my_blob</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="291" style="width: 35px; color: rgba(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="LC291" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="270" style="width: 35px; color: rgba(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="LC292" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># just create an empty file with the right timestamps</span></span>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python">            <span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_properties</span><span class="p">().</span><span class="n" style="color: #333;">last_modified</span><span class="p">.</span><span class="n" style="color: #333;">timestamp</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC294" 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;">destination_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fp</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python">                <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">utime</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python">                    <span class="n" style="color: #333;">fp</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">ts</span><span class="p">,</span> <span class="n" style="color: #333;">ts</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python">                <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC271" 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="LC272" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># just create an empty file with the right timestamps</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC273" 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;">destination_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fp</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python">                    <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">utime</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;">fp</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python">                        <span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">last_modified</span><span class="p">.</span><span class="n" style="color: #333;">timestamp</span><span class="p">(),</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">last_modified</span><span class="p">.</span><span class="n" style="color: #333;">timestamp</span><span class="p">()),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python">                    <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">destination_path</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">destination_path</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="300" style="width: 35px; color: rgba(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="LC300" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">delete_from_container</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python">        <span class="s" style="color: #d14;">""" Delete a file from Azure Storage container</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -293,8 +311,8 @@ class AzureStorageHelper(object):</td>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"container_name must be specified"</span></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">blob_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"blob_name must be specified"</span></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python">        <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">azure</span></span></span>

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python">        <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">delete_blob</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">container_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">blob_name</span></span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python">        <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">blob_service_client</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_blob_client</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">container_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">blob_name</span></span><span class="p"><span class="idiff right">)</span></span></span>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python">        <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">delete_blob</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">exists_in_container</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python">        <span class="s" style="color: #d14;">""" Returns whether the blob exists in the container</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">@@ -306,12 +324,13 @@ class AzureStorageHelper(object):</td>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"><span class="s" style="color: #d14;">            Returns:</span></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"><span class="s" style="color: #d14;">                True | False</span></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"container_name must be specified"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"></span>

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<td class="diff-line-num new old_line" data-linenumber="310" style="width: 35px; color: rgba(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="LC328" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="310" style="width: 35px; color: rgba(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="LC329" class="line" lang="python">            <span class="n" style="color: #333;">container_name</span></span>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python">        <span class="p">),</span> <span class="s" style="color: #d14;">'container_name must be specified (did you try to write to "root" or forgot to set --default-remote-prefix?)'</span></span>

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<td class="diff-line-num old_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">blob_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"blob_name must be specified"</span></span>

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<pre style="margin: 0;">-<span id="LC311" 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="LC312" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">azure</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python">        <span class="n" style="color: #333;">cc</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob_service_client</span><span class="p">.</span><span class="n" style="color: #333;">get_container_client</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(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="LC333" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="bp" style="color: #999;">True</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cc</span><span class="p">.</span><span class="n" style="color: #333;">list_blobs</span><span class="p">(</span><span class="n" style="color: #333;">name_starts_with</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">blob_name</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">blob_size</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python">        <span class="s" style="color: #d14;">""" Returns the size of a blob</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="326" style="width: 35px; color: rgba(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">@@ -326,12 +345,8 @@ class AzureStorageHelper(object):</td>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"container_name must be specified"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">blob_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"blob_name must be specified"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python">            <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">azure</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_properties</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="p">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">properties</span><span class="p">.</span><span class="n" style="color: #333;">content_length</span> <span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">1024</span></span>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"blob or container do not exist"</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python">        <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob_service_client</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_client</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_properties</span><span class="p">().</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">1024</span></span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">blob_last_modified</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python">        <span class="s" style="color: #d14;">""" Returns a timestamp of a blob</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="345" style="width: 35px; color: rgba(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">@@ -345,12 +360,8 @@ class AzureStorageHelper(object):</td>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"container_name must be specified"</span></span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">blob_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"blob_name must be specified"</span></span>

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<pre style="margin: 0;">-<span id="LC348" 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="LC349" class="line" lang="python">            <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">azure</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_properties</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">properties</span><span class="p">.</span><span class="n" style="color: #333;">last_modified</span><span class="p">.</span><span class="n" style="color: #333;">timestamp</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"blob or container do not exist"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python">        <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob_service_client</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_client</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_properties</span><span class="p">().</span><span class="n" style="color: #333;">last_modified</span><span class="p">.</span><span class="n" style="color: #333;">timestamp</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">list_blobs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">container_name</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python">        <span class="s" style="color: #d14;">""" Returns a list of blobs from the container</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="362" style="width: 35px; color: rgba(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="373" style="width: 35px; color: rgba(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">@@ -362,9 +373,5 @@ class AzureStorageHelper(object):</td>

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"><span class="s" style="color: #d14;">                list of blobs</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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"container_name must be specified"</span></span>

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<pre style="margin: 0;">-<span id="LC365" 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="LC366" class="line" lang="python">            <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">azure</span><span class="p">.</span><span class="n" style="color: #333;">list_blobs</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">o</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">b</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC368" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Did you provide a valid container_name?"</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC370" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span></pre>

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python">        <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob_service_client</span><span class="p">.</span><span class="n" style="color: #333;">get_container_client</span><span class="p">(</span><span class="n" style="color: #333;">container_name</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">list_blobs</span><span class="p">()]</span></span></pre>

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<br>

</li>

<li id="7e910b8868374c8ee0002ac6d034da0012544b27">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#7e910b8868374c8ee0002ac6d034da0012544b27"><strong>snakemake/remote/GS.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">@@ -18,10 +18,10 @@ try:</td>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python">    <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">google.cloud</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">google.cloud</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">storage</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">google.api_core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">retry</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;"><span class="idiff left">crc32c</span></span><span class="idiff"> </span><span class="kn" style="font-weight: 600;"><span class="idiff">import</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">crc32</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(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="LC21" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;"><span class="idiff left">google_crc32c</span></span><span class="idiff"> </span><span class="kn" style="font-weight: 600;"><span class="idiff">import</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Checksum</span></span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python">    <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python">        <span class="s" style="color: #d14;">"The Python 3 packages 'google-cloud-sdk' and `crc32c` "</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">        <span class="s" style="color: #d14;">"The Python 3 packages 'google-cloud-sdk' and `<span class="idiff left right">google-</span>crc32c` "</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python">        <span class="s" style="color: #d14;">"need to be installed to use GS remote() file functionality. %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">msg</span></span>

</pre>

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

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,7 +56,7 @@ class Crc32cCalculator:</td>

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

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

</pre>

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

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<pre style="margin: 0;"> <span id="LC57" 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;">fileobj</span><span class="p">):</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_fileobj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileobj</span></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">digest</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">checksum</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Checksum</span></span><span class="p"><span class="idiff right">()</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(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="LC60" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(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="LC61" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">chunk</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_fileobj</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">chunk</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">@@ -65,14 +65,14 @@ class Crc32cCalculator:</td>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_update</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">chunk</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python">        <span class="s" style="color: #d14;">"""Given a chunk from the read in file, update the hexdigest</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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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="p">.</span><span class="n" style="color: #333;"><span class="idiff left">digest</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">crc32</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">chunk</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">digest</span></span><span class="p">)</span></span>

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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="p">.</span><span class="n" style="color: #333;"><span class="idiff left">checksum</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">update</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">chunk</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">hexdigest</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="LC71" class="line" lang="python">        <span class="s" style="color: #d14;">"""Return the hexdigest of the hasher.</span></span>

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<td class="diff-line-num new_line" data-linenumber="72" style="width: 35px; color: rgba(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="LC72" class="line" lang="python"><span class="s" style="color: #d14;">           The Base64 encoded CRC32c is in big-endian byte order.</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"><span class="s" style="color: #d14;">           See https://cloud.google.com/storage/docs/hashes-etags</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">base64</span><span class="p">.</span><span class="n" style="color: #333;">b64encode</span><span class="p">(</span><span class="n" style="color: #333;">s<span class="idiff left">truct</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pack</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">">I"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">digest</span></span><span class="p">)).</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">"utf-8"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">base64</span><span class="p">.</span><span class="n" style="color: #333;">b64encode</span><span class="p">(</span><span class="bp" style="color: #999;">s<span class="idiff left">elf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">checksum</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">digest</span></span><span class="p"><span class="idiff right">(</span>)).</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">"utf-8"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"></span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">RemoteProvider</span><span class="p">(</span><span class="n" style="color: #333;">AbstractRemoteProvider</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">@@ -138,17 +138,17 @@ class RemoteObject(AbstractRemoteObject):</td>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"><span class="s" style="color: #d14;">            - cache_mtime</span></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"><span class="s" style="color: #d14;">            - cache.size</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">blob</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">client</span><span class="p">.</span><span class="n" style="color: #333;">list_blobs</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">bucket_name</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python">        <span class="p">):</span></span>

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<td class="diff-line-num new old_line" data-linenumber="144" style="width: 35px; color: rgba(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="LC141" class="line" lang="python">        <span class="n" style="color: #333;">subfolder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">blob</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">client</span><span class="p">.</span><span class="n" style="color: #333;">list_blobs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">bucket_name</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subfolder</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># By way of being listed, it exists. mtime is a datetime object</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python">            <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="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="n" style="color: #333;">bucket</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python">            <span class="n" style="color: #333;">cache</span><span class="p">.</span><span class="n" style="color: #333;">exists_remote</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python">            <span class="n" style="color: #333;">cache</span><span class="p">.</span><span class="n" style="color: #333;">mtime</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="n" style="color: #333;">updated</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python">            <span class="n" style="color: #333;">cache</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="n" style="color: #333;">size</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Mark bucket as having an inventory, such that this method is</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># only called once for this bucket.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python">        <span class="n" style="color: #333;">cache</span><span class="p">.</span><span class="n" style="color: #333;">has_inventory</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">bucket_name</span><span class="p">)</span></span>

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

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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(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="LC149" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Mark bucket and prefix as having an inventory, such that this method is</span></span>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># only called once for the subfolder in the bucket.</span></span>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python">        <span class="n" style="color: #333;">cache</span><span class="p">.</span><span class="n" style="color: #333;">has_inventory</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"%s/%s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">bucket_name</span><span class="p">,</span> <span class="n" style="color: #333;">subfolder</span><span class="p">))</span></span>

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

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># === Implementations of abstract class members ===</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="173" style="width: 35px; color: rgba(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">@@ -173,8 +173,10 @@ class RemoteObject(AbstractRemoteObject):</td>

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<pre style="margin: 0;"> <span id="LC173" 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="LC174" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_iofile</span><span class="p">.</span><span class="n" style="color: #333;">size_local</span></span>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">retry</span><span class="p">.</span><span class="n" style="color: #333;">Retry</span><span class="p">(</span><span class="n" style="color: #333;">predicate</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">google_cloud_retry_predicate</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">retry</span><span class="p">.</span><span class="n" style="color: #333;">Retry</span><span class="p">(</span><span class="n" style="color: #333;">predicate</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">google_cloud_retry_predicate</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">deadline</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">600</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">download</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="LC178" class="line" lang="python">        <span class="s" style="color: #d14;">"""Download with maximum retry duration of 600 seconds (10 minutes)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">():</span></span>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="188" style="width: 35px; color: rgba(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="190" style="width: 35px; color: rgba(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">@@ -188,6 +190,9 @@ class RemoteObject(AbstractRemoteObject):</td>

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<td class="diff-line-num old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

188

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<td class="diff-line-num new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

190

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="n" style="color: #333;">download_to_file</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

189

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<td class="diff-line-num new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

191

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sync</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

190

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<td class="diff-line-num new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

192

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

193

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># **Important** hash can be incorrect or missing if not refreshed</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

194

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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="p">.</span><span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="nb" style="color: #0086b3;">reload</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

195

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

191

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<td class="diff-line-num new_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">

196

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Compute local hash and verify correct</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

192

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<td class="diff-line-num new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

197

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="n" style="color: #333;">crc32c</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

193

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<td class="diff-line-num new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

198

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python">            <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_file</span><span class="p">())</span></span>

</pre>

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<br>

</li>

<li id="1ffa1b3765afe0782e1886aa5b41999ae4d03543">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#1ffa1b3765afe0782e1886aa5b41999ae4d03543"><strong>snakemake/resources.py</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,9 +7,13 @@ class DefaultResources:</td>

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7

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

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>

</pre>

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

8

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

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fallback</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">):</span></span>

</pre>

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

9

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

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python">            <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">callable</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="p">,</span> <span class="n" style="color: #333;">attempt</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="p">,</span> <span class="n" style="color: #333;">rulename</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python">                <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">eval</span><span class="p">(</span></span>

</pre>

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11

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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python">                    <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"input"</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">input</span><span class="p">,</span> <span class="s" style="color: #d14;">"attempt"</span><span class="p">:</span> <span class="n" style="color: #333;">attempt</span><span class="p">,</span> <span class="s" style="color: #d14;">"threads"</span><span class="p">:</span> <span class="n" style="color: #333;">threads</span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python">                <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python">                    <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">eval</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python">                        <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"input"</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">input</span><span class="p">,</span> <span class="s" style="color: #d14;">"attempt"</span><span class="p">:</span> <span class="n" style="color: #333;">attempt</span><span class="p">,</span> <span class="s" style="color: #d14;">"threads"</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="LC13" class="line" lang="python">                    <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Triggers for string arguments like n1-standard-4</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">NameError</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">                    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">val</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">callable</span></span>

</pre>

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</li>

<li id="d1deee71de70305809d43086b13f7eb407aff6f2">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#d1deee71de70305809d43086b13f7eb407aff6f2"><strong>test-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">@@ -30,8 +30,7 @@ dependencies:</td>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">google-cloud-storage</span></span>

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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;">google-api-python-client</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;">oauth2client</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;">azure-storage</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;">azure-storage-common</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;">azure-storage-blob</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;">ratelimiter</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">configargparse</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">appdirs</span></span>

</pre>

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</li>

<li id="18051d6fa83e6daf8ee96c3f5093a8d27095f4fa">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#18051d6fa83e6daf8ee96c3f5093a8d27095f4fa"><strong>tests/common.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">@@ -147,6 +147,7 @@ def run(</td>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python">        <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python">        <span class="n" style="color: #333;">verbose</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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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python">        <span class="n" style="color: #333;">conda_frontend</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">conda_frontend</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python">        <span class="n" style="color: #333;">container_image</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">container_image</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python">        <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">params</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"></span>

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<br>

</li>

<li id="d67f606b4bee14c69feeb3f0aa59bb04fdd7bd36">

<a href="https://salsa.debian.org/med-team/snakemake/-/commit/ede461d574af316927b0b43b0637e75795ba0d17#d67f606b4bee14c69feeb3f0aa59bb04fdd7bd36"><strong>tests/test_remote_azure/Snakefile</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,16 +2,11 @@ import os</td>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">import fnmatch</span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">import snakemake</span>

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">from snakemake.exceptions import MissingInputException</span>

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5

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">from snakemake.remote.Az<span class="idiff left right">ureStorage</span> import RemoteProvider as AzureRemoteProvider</span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">from snakemake.remote.Az<span class="idiff left right">Blob</span> import RemoteProvider as AzureRemoteProvider</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="LC7" class="line" lang="plaintext"># setup Azure Storage for remote access</span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># for testing these variable can be added to CircleCI</span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">account_name=os.environ['AZURE_ACCOUNT']</span>

</pre>

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10

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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">account_key=os.environ.get('AZURE_KEY')</span>

</pre>

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11

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">sas_token=os.environ.get('SAS_TOKEN')</span>

</pre>

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12

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">assert sas_token or account_key, ("Either SAS_TOKEN or AZURE_KEY have to be set")</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">AS = AzureRemoteProvider(account_name=account_name,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">    account_key=account_key, sas_token=sas_token)</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"># for testing, set AZ_AZURE_ACCOUNT and AZ_ACCOUNT_KEY or AZ_SAS_TOKEN as env vars to CircleCI</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">AS = AzureRemoteProvider()</span>

</pre>

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

15

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

</pre>

</td>

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

16

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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

</pre>

</td>

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

17

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

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">rule upload_to_azure_storage:</span>

</pre>

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