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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/covpipe">Debian Med / covpipe</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250">f50c03dc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-15T09:38:43+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.6</pre>
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<h4>26 changed files:</h4>
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.conda/3.0.3/build.sh
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.conda/3.0.3/meta.yaml
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.conda/3.0.4/build.sh
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.conda/3.0.4/meta.yaml
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.conda/3.0.5/build.sh
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.conda/3.0.5/meta.yaml
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.conda/meta.yaml
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.gitlab-ci.yml
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<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#597ee46638e91ade71d0651e36532ab84c30fcb1">
covpipe/__version__.py
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<a href="#72689fc391b930e2f46a05a96f44728e8f62876d">
covpipe/ncov_minipipe.Rmd
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<a href="#d051687e18203812decae43018b3bd6ecf28804f">
covpipe/ncov_minipipe.config
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<a href="#622a6ad92f0f17016033d2e2a3034b6709a24faf">
covpipe/ncov_minipipe.py
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covpipe/ncov_minipipe.snake
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<a href="#80f2e49a40c26133b9b6bcdfcf08efdfa2247a37">
covpipe/rules/assign_lineage.smk
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covpipe/rules/classify_reads.smk
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<a href="#d775516cdb3f3ec1ad8cb5e542e7cab3c007df47">
covpipe/rules/get_version.smk
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<a href="#dca120fe48a8f069b9b95e3209aa9f51daccc7d9">
covpipe/rules/trim_reads.smk
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<a href="#4b2465b2029aef2dcee63d208c5b8609d5678dbd">
covpipe_env.yaml
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covpipe_tools/primerbed2bedpe.py
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covpipe_tools/update_pangolin.py
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<a href="#97d42055d8a8ae104887701fdda7934b652e6192">
ncov_minipipe.conda.setup/setup_env.sh
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<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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tests/TestData/GEN_SAMPLES/mixture.csv
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<a href="#1ae8c96e8d5c628787ec4ee9c13d9c7baf1b2d4a">
tests/quicktest.sh
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<h4>Changes:</h4>
<li id="c0d67716a4ccb1ddb1295b3168e55a5279d1baa4">
<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#c0d67716a4ccb1ddb1295b3168e55a5279d1baa4"><strong>.conda/3.0.3/build.sh</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">$PYTHON</span> setup.py <span class="nb" style="color: #0086b3;">install</span> </span></pre>
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<li id="9306975c462aacafd98eb240ab148e59789541f3">
<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#9306975c462aacafd98eb240ab148e59789541f3"><strong>.conda/3.0.3/meta.yaml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="pi">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="nv" style="color: #008080;">set version = "3.0.3" %</span><span class="pi">}</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">package</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">covpipe</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="pi">{{</span> <span class="nv" style="color: #008080;">version</span> <span class="pi">}}</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">source</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">git_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe.git</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">git_rev</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">v{{</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">version</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">}}"</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">number</span><span class="pi">:</span> <span class="s" style="color: #d14;">0</span> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">requirements</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">host</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">snakemake >=5.26</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">strictyaml</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pandas</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">about</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">home</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe.git</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">license</span><span class="pi">:</span> <span class="s" style="color: #d14;">GPLv3</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">summary</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Sars-Cov-2</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">NGS</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Pipeline'</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">description</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="s" style="color: #d14;">NGS Anlysis of Sars-Cov-2 </span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">dev_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">doc_source_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe/-/blob/v{{ version }}/README.md</span> </span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">$PYTHON</span> setup.py <span class="nb" style="color: #0086b3;">install</span> </span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="pi">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="nv" style="color: #008080;">set version = "3.0.4" %</span><span class="pi">}</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">package</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">covpipe</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="pi">{{</span> <span class="nv" style="color: #008080;">version</span> <span class="pi">}}</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">source</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">git_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe.git</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">git_rev</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">v{{</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">version</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">}}"</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">number</span><span class="pi">:</span> <span class="s" style="color: #d14;">0</span> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">requirements</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">host</span><span class="pi">:</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">snakemake >=5.26</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">strictyaml</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pandas</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">about</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">home</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe.git</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">license</span><span class="pi">:</span> <span class="s" style="color: #d14;">GPLv3</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">summary</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Sars-Cov-2</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">NGS</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Pipeline'</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">description</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="s" style="color: #d14;">NGS Anlysis of Sars-Cov-2 </span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">dev_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">doc_source_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe/-/blob/v{{ version }}/README.md</span> </span></pre>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#e8981d8aba3d5776b234404fe87a235b30f1b4f3"><strong>.conda/3.0.5/build.sh</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">$PYTHON</span> setup.py <span class="nb" style="color: #0086b3;">install</span> </span></pre>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#a2c1f4fd11af11ac9c8c713cbbb49881538362ac"><strong>.conda/3.0.5/meta.yaml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="pi">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="nv" style="color: #008080;">set version = "3.0.5" %</span><span class="pi">}</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">package</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">covpipe</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="pi">{{</span> <span class="nv" style="color: #008080;">version</span> <span class="pi">}}</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">source</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">git_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe.git</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">git_rev</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">v{{</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">version</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">}}"</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">number</span><span class="pi">:</span> <span class="s" style="color: #d14;">0</span> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">requirements</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">host</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">snakemake >=5.26</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">strictyaml</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pandas</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">about</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">home</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe.git</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">license</span><span class="pi">:</span> <span class="s" style="color: #d14;">GPLv3</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">summary</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Sars-Cov-2</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">NGS</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Pipeline'</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">description</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="s" style="color: #d14;">NGS Anlysis of Sars-Cov-2 </span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">dev_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">doc_source_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe/-/blob/v{{ version }}/README.md</span> </span></pre>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#d257ba2aa1e53f638eeeafd0740bb03d350917fc"><strong>.conda/meta.yaml</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="pi">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="nv" style="color: #008080;">set version = "3.0.<span class="idiff left right">3</span>" %</span><span class="pi">}</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="pi">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="nv" style="color: #008080;">set version = "3.0.<span class="idiff left right">6</span>" %</span><span class="pi">}</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">package</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">covpipe</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="pi">{{</span> <span class="nv" style="color: #008080;">version</span> <span class="pi">}}</span></span>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#587d266bb27a4dc3022bbed44dfa19849df3044c"><strong>.gitlab-ci.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">@@ -5,22 +5,26 @@ cache:</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$CI_PROJECT_DIR/.conda_cache</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$CI_PROJECT_DIR/.apt_cache</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">before_script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda update -y -n base conda</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda install -y -c conda-forge mamba</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mamba update -y -n base conda</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mamba install -y conda-build</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export APT_DIR=$CI_PROJECT_DIR/.apt_cache && export APT_STATE_LISTS=$APT_DIR/lists && export APT_CACHE_ARCHIVES=$APT_DIR/archives</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">printf "dir::state::lists ${APT_STATE_LISTS};\ndir::cache::archives ${APT_CACHE_ARCHIVES};\n" > /etc/apt/apt.conf</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir -p "${APT_STATE_LISTS}/partial" && mkdir -p "${APT_CACHE_ARCHIVES}/partial"</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">stages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - build_env</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">quicktest</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pypi-gitlab</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git-release</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - simple_amplidata_test</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">test</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">build_pypackage</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">migrate_to_prerelease</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">deploy_git_release</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">deploy_pypi_upload</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">deploy_gitlab_index_upload</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">deploy_docker_build</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#simple_amplidata_test:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># stage: <span class="idiff left right">simple_amplidata_</span>test</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># stage: test</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># timeout: 1h</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># script:</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - ./tests/simple_amplidata_test/test.sh</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,6 +40,7 @@ stages:</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="yaml"><span class="na" style="color: #008080;">quicktest</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">development_unstable</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">test_pre_release</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pre_release</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">next_milestone</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span></span>
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<td class="diff-line-num unfold js-unfold new_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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,47 +57,128 @@ quicktest:</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">tests/QuickTest/test02/sample.config.yaml"</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">tests/QuickTest/test03/output/sample.config.yaml"</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="yaml"><span class="na" style="color: #008080;">upload_gitlab_pypi</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="yaml"><span class="na" style="color: #008080;">build_pip</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span> </span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypi-gitlab</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">stage_pip_release</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">build_pypackage</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;"><span class="idiff left right">pip install twine</span></span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;"><span class="idiff left">mamba env update -n base -f covpipe_env.yaml</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py sdist bdist_wheel</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">TWINE_PASSWORD=${CI_JOB_TOKEN} TWINE_USERNAME=gitlab-ci-token python -m twine upload --repository-url https://gitlab.com/api/v4/projects/${CI_PROJECT_ID}/packages/pypi dist/*</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">TWINE_PASSWORD=${PYPI_RELEASE_TOKEN} TWINE_USERNAME=__token__ python -m twine upload --repository-url https://upload.pypi.org/legacy/ dist/*</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="yaml"> <span class="na" style="color: #008080;">artifacts</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="yaml"> <span class="na" style="color: #008080;">paths</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">dist/*</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="yaml"><span class="na" style="color: #008080;">build_docker</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="yaml"> <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">docker:19.03.12</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="yaml"> <span class="na" style="color: #008080;">services</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docker:19.03.12-dind</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">stage_docker_build</span> </span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">git-release</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="yaml"> <span class="na" style="color: #008080;">before_script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo "Do Nothing"</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docker build -t registry.gitlab.com/rkibioinformaticspipelines/ncov_minipipe .</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docker push registry.gitlab.com/rkibioinformaticspipelines/ncov_minipipe -p</span> </span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="yaml"><span class="na" style="color: #008080;">make_new_release</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">git<span class="idiff left right">-</span>release</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left">deploy_</span>git<span class="idiff right">_</span>release</span></span>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="yaml"> <span class="na" style="color: #008080;">before_script</span><span class="pi">:</span></span>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">apt-get update</span></span>
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86
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">apt-get -y install software-properties-common</span></span>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">apt-get update</span></span>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">apt-get -y install php php-json git openssh-client curl</span></span>
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89
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">VERSION="$( git tag | grep -E 'v[0-9]+\.[0-9]+\.[0-9]+$' | tail -n1 )"</span> </span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git fetch --tags origin</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">VERSION="$( git tag -l | grep -E 'v[0-9]+\.[0-9]+\.[0-9]+$' | tail -n1 )"</span> </span>
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91
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">DESCRIPTION="$( git cat-file -p $VERSION )"</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">MESSAGE="$(php -r "echo json_encode(['name' => '$VERSION', 'tag_name' => '$VERSION', 'description' => '$DESCRIPTION']);")";</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">SAFE_DESCR="$(sed 's/\([^\\]\)'"'"'/\1\\'"'/g" <<< "$DESCRIPTION")"</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">MESSAGE="$(php -r "echo json_encode(['name' => '$VERSION', 'tag_name' => '$VERSION', 'description' => '$SAFE_DESCR']);")";</span></span>
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93
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo $MESSAGE</span></span>
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94
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="yaml"> <span class="pi">-</span> <span class="pi">></span></span>
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95
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="yaml"> <span class="s" style="color: #d14;">curl --header 'Content-Type: application/json' --header "JOB-TOKEN: ${CI_JOB_TOKEN}" \</span></span>
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96
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="yaml"> <span class="s" style="color: #d14;">--data "$MESSAGE" \</span></span>
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97
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="yaml"> <span class="s" style="color: #d14;">--request POST ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/releases</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="yaml"> </span></pre>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="yaml"></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="yaml"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="yaml"><span class="na" style="color: #008080;">trigger_pre_release</span><span class="pi">:</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">test_pre_release</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">migrate_to_prerelease</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir -pvm 0700 $HOME/.ssh</span></span>
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<td class="new_line diff-line-num new" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ssh-keyscan -t rsa gitlab.com >> $HOME/.ssh/known_hosts</span></span>
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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo "$NeedToKnow" > $HOME/.ssh/id_rsa-gitlab-ci</span></span>
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<td class="new_line diff-line-num new" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ls -la $HOME/.ssh/id_rsa-gitlab-ci</span></span>
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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">chmod 0400 $HOME/.ssh/id_rsa-gitlab-ci</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git fetch</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git checkout pre_release</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git remote set-url --push origin $(perl -pe 's#.*@(.+?(\:\d+)?)/#git@\1:#' <<< $CI_REPOSITORY_URL)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git remote -v</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git merge origin/test_pre_release --no-edit</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">GIT_SSH_COMMAND="ssh -o StrictHostKeyChecking=no -i $HOME/.ssh/id_rsa-gitlab-ci" git push</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="yaml"> <span class="na" style="color: #008080;">after_script</span><span class="pi">:</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">rm -Rfv .ssh</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="yaml"></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="yaml"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="yaml"><span class="na" style="color: #008080;">trigger_pypi_stage</span><span class="pi">:</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">deploy_git_release</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir -pvm 0700 $HOME/.ssh</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ssh-keyscan -t rsa gitlab.com >> $HOME/.ssh/known_hosts</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo "$NeedToKnow" > $HOME/.ssh/id_rsa-gitlab-ci</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ls -la $HOME/.ssh/id_rsa-gitlab-ci</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">chmod 0400 $HOME/.ssh/id_rsa-gitlab-ci</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git fetch</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git checkout stage_pip_release</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git remote set-url --push origin $(perl -pe 's#.*@(.+?(\:\d+)?)/#git@\1:#' <<< $CI_REPOSITORY_URL)</span></span>
</pre>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git remote -v</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git merge origin/master --no-edit</span></span>
</pre>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">GIT_SSH_COMMAND="ssh -o StrictHostKeyChecking=no -i $HOME/.ssh/id_rsa-gitlab-ci" git push</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="yaml"> <span class="na" style="color: #008080;">after_script</span><span class="pi">:</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">rm -Rfv .ssh</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="yaml"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="yaml"><span class="na" style="color: #008080;">trigger_docker_stage</span><span class="pi">:</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">deploy_git_release</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir -pvm 0700 $HOME/.ssh</span></span>
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<td class="new_line diff-line-num new" 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">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ssh-keyscan -t rsa gitlab.com >> $HOME/.ssh/known_hosts</span></span>
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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo "$NeedToKnow" > $HOME/.ssh/id_rsa-gitlab-ci</span></span>
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<td class="new_line diff-line-num new" 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">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ls -la $HOME/.ssh/id_rsa-gitlab-ci</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">chmod 0400 $HOME/.ssh/id_rsa-gitlab-ci</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git fetch</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git checkout stage_docker_release</span></span>
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<td class="new_line diff-line-num new" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git remote set-url --push origin $(perl -pe 's#.*@(.+?(\:\d+)?)/#git@\1:#' <<< $CI_REPOSITORY_URL)</span></span>
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<td class="new_line diff-line-num new" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git remote -v</span></span>
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<td class="new_line diff-line-num new" 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">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git merge origin/master --no-edit</span></span>
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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">GIT_SSH_COMMAND="ssh -o StrictHostKeyChecking=no -i $HOME/.ssh/id_rsa-gitlab-ci" git push</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="yaml"> <span class="na" style="color: #008080;">after_script</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num new" 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="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">rm -Rfv .ssh</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="yaml"></span>
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<td class="new_line diff-line-num new" 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="yaml"><span class="na" style="color: #008080;">upload_gitlab_pypi</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span> </span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">stage_pip_release</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">deploy_git_release</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install twine</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">TWINE_PASSWORD=${CI_JOB_TOKEN} TWINE_USERNAME=gitlab-ci-token python -m twine upload --repository-url https://gitlab.com/api/v4/projects/${CI_PROJECT_ID}/packages/pypi dist/*</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="yaml"><span class="na" style="color: #008080;">upload_pypi</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span> </span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">stage_pip_release</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">deploy_pypi_upload</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install twine</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">TWINE_PASSWORD=${PYPI_RELEASE_TOKEN} TWINE_USERNAME=__token__ python -m twine upload --repository-url https://upload.pypi.org/legacy/ dist/*</span></span>
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170
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171
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="yaml"><span class="na" style="color: #008080;">build_docker</span><span class="pi">:</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="yaml"> <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">docker:19.03.12</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="yaml"> <span class="na" style="color: #008080;">services</span><span class="pi">:</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docker:19.03.12-dind</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">stage_docker_release</span> </span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">deploy_docker_build</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="yaml"> <span class="na" style="color: #008080;">before_script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo "Do Nothing"</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY</span></span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docker build -t registry.gitlab.com/rkibioinformaticspipelines/ncov_minipipe .</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docker push registry.gitlab.com/rkibioinformaticspipelines/ncov_minipipe</span> </span></pre>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#6651ddff6eb82c840ced7c1dddee15c6e1913dd4"><strong>Dockerfile</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> continuumio/miniconda3</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> VERSION 3.0.<span class="idiff left right">1.post2</span></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> VERSION 3.0.<span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> TOOL covpipe</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># meta data</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -11,32 +11,31 @@ LABEL about.home="https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe"</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> maintainer="RKI MF1 Bioinformatics <https://www.rki.de/EN/Content/Institute/DepartmentsUnits/MF/MF1/mf1_node.html>"</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="docker"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># install basics</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt update <span class="o" style="font-weight: 600;">&&</span> apt <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> procps wget <span class="nb" style="color: #0086b3;">gzip </span>pigz bc build-essential libbz2-dev <span class="o" style="font-weight: 600;">&&</span> apt-get clean <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> /var/lib/apt/lists/<span class="k" style="font-weight: 600;">*</span> /tmp/<span class="k" style="font-weight: 600;">*</span> /var/tmp/<span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>pip <span class="nb" style="color: #0086b3;">install </span>Cython</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>conda <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-c</span> bioconda <span class="nt" style="color: #000080;">-c</span> conda-forge <span class="nv" style="color: #008080;">python</span><span class="o" style="font-weight: 600;">=</span>3.7 mamba</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="docker"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># install covpipe latest version</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>pip <span class="nb" style="color: #0086b3;">install </span><span class="nv" style="color: #008080;">covpipe</span><span class="o" style="font-weight: 600;">==</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">VERSION</span><span class="k" style="font-weight: 600;">}</span> </span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># install basics & covpipe</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt update <span class="o" style="font-weight: 600;">&&</span> apt <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> procps wget <span class="nb" style="color: #0086b3;">gzip </span>pigz bc build-essential libbz2-dev <span class="o" style="font-weight: 600;">&&</span> apt-get clean <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> /var/lib/apt/lists/<span class="k" style="font-weight: 600;">*</span> /tmp/<span class="k" style="font-weight: 600;">*</span> /var/tmp/<span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>pip <span class="nb" style="color: #0086b3;">install </span>Cython <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> conda <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-c</span> bioconda <span class="nt" style="color: #000080;">-c</span> conda-forge <span class="nv" style="color: #008080;">python</span><span class="o" style="font-weight: 600;">=</span>3.7 mamba <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> pip <span class="nb" style="color: #0086b3;">install </span><span class="nv" style="color: #008080;">covpipe</span><span class="o" style="font-weight: 600;">==</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">VERSION</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> mamba clean <span class="nt" style="color: #000080;">-a</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">chmod</span> <span class="nt" style="color: #000080;">-R</span> a+w /opt/conda</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># install all environments according to snakemakes default path and hashing procedure</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="docker"><span class="k" style="font-weight: 600;">COPY</span><span class="s" style="color: #d14;"> hash.py . </span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">chmod</span> +x hash.py</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="docker"><span class="k" style="font-weight: 600;"><span class="idiff left right">RUN</span> for </span>YAML <span class="k" style="font-weight: 600;">in</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> /opt/conda/lib/python3.7/site-packages/covpipe/envs/<span class="k" style="font-weight: 600;">*</span>.yaml<span class="si" style="color: #d14;">)</span><span class="p">;</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">chmod</span> +x hash.py<span class="idiff left"> </span><span class="se" style="color: #d14;"><span class="idiff right">\</span></span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="docker"><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">&&</span></span> <span class="k" style="font-weight: 600;">for </span>YAML <span class="k" style="font-weight: 600;">in</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> /opt/conda/lib/python3.7/site-packages/covpipe/envs/<span class="k" style="font-weight: 600;">*</span>.yaml<span class="si" style="color: #d14;">)</span><span class="p">;</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="docker"> <span class="k" style="font-weight: 600;">do </span><span class="nb" style="color: #0086b3;">export </span>YAML<span class="p">;</span> <span class="nv" style="color: #008080;">MD5</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>python hash.py | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-c</span> 1-8<span class="si" style="color: #d14;">)</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> mamba <span class="nb" style="color: #0086b3;">env </span>create <span class="nt" style="color: #000080;">--prefix</span> /.snakemake/conda/<span class="nv" style="color: #008080;">$MD5</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$YAML</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> /tmp/<span class="k" style="font-weight: 600;">*</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> /root/.conda/pkgs/<span class="k" style="font-weight: 600;">*</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> /opt/conda/pkgs/<span class="k" style="font-weight: 600;">*</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cp</span> <span class="nv" style="color: #008080;">$YAML</span> /.snakemake/conda/<span class="nv" style="color: #008080;">$MD5</span>.yaml<span class="p">;</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="docker"> <span class="k" style="font-weight: 600;">done</span> </span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="docker"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># clean conda (keep image at least a bit smaller)</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>conda clean <span class="nt" style="color: #000080;">-a</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="docker"> <span class="k" style="font-weight: 600;">done</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> mamba clean <span class="nt" style="color: #000080;">-a</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">chmod</span> <span class="nt" style="color: #000080;">-R</span> a+w /opt/conda <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">chmod</span> <span class="nt" style="color: #000080;">-R</span> a+w /.snakemake</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># integrate kraken database into the container (will increase container size by ~4 GB!)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>wget <span class="nt" style="color: #000080;">-q</span> <span class="nt" style="color: #000080;">-O</span> kraken_db.tar.gz https://zenodo.org/record/4534746/files/GRCh38.p13_SC2_2021-02-08.tar.gz?download<span class="o" style="font-weight: 600;">=</span>1</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">tar </span>zxvf kraken_db.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">rm </span>kraken_db.tar.gz</span></pre>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>wget <span class="nt" style="color: #000080;">-q</span> <span class="nt" style="color: #000080;">-O</span> kraken_db.tar.gz https://zenodo.org/record/4534746/files/GRCh38.p13_SC2_2021-02-08.tar.gz?download<span class="o" style="font-weight: 600;">=</span>1 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">tar </span>zxvf kraken_db.tar.gz <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">rm </span>kraken_db.tar.gz <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">chmod</span> <span class="nt" style="color: #000080;">-R</span> a+rX /GRCh38.p13_SC2_2021-02-08</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">@@ -224,9 +224,40 @@ the same for the inserts, you can transform this into the desired bed file.</td>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="markdown">create_bedpe AMPLICON_FILE.bed INSERT_FILE.bed <span class="nt" style="color: #000080;">-o</span> myPrimerPositions.bedpe</span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 4.<span class="idiff left right">3 Activating taxonomic read filtering</span></span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##<span class="idiff left">#</span> 4.<span class="idiff right">2.2 Create bedpe from primer bed file</span></span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 4.3 Activating taxonomic Read Filtering</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="markdown">You might have a primer bed file, like the one provided in the artic repository.</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="markdown">If the primer names have clear identifiers for forward and reverse primers youb can use the following script.</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="markdown">bed2bedpe nCoV-2019.primer.bed <span class="nt" style="color: #000080;">--output</span> nCoV-2019.primer.bedpe</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="markdown">Take care: If you use artic you need to change the reference name to NC_045512.2, when using our default settings. </span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 4.3 Adjusting Read Filtering</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 4.3.1 Read Length</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown">Per default the minimum read length filter is set to 50. </span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="markdown">We chose this, because we designed the pipeline with 159 BP pared end amplicons in mind. </span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="markdown">We actually encountered a bunch of primer dimers that were shorter than 50 BP</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="markdown">and found them enough of a nuisance to take this step.</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="markdown">(Quick aside: We use the mapping rate as a quick quality measure and that gets polluted by the dimers.) </span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown">If you are using shorter amplicóns in your protocol, you will most likely need</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="markdown">to set this option to something lower.</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="markdown">(--filter_read_len 25) </span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 4.3.2 Read Quality</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="markdown">Qualitative read quality used by fastp to filter reads.</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="markdown">By default the "--read_filter_qual" option uses a phredscore of 20 as a cutoff.</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="markdown">Prior to version 3.0.4 it was hard coded to 15. </span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="markdown">If you want to recreate your pipeline runs from prior versions, set this option</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="markdown">to 15. </span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 4.4 Activating taxonomic Read Filtering</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="markdown">If necessary, reads not derived from SARS-COV-2 can be excluded. </span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="markdown">Read classification is based on corresponding k-mer frequencies using a defined kraken2 database (<span class="sb" style="color: #d14;">`--kraken`</span>). </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="246" style="width: 35px; color: rgba(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="277" style="width: 35px; color: rgba(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">@@ -246,7 +277,7 @@ ncov_minipipe --kraken path/to/myKrakenDbFolder \</td>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-o</span> path/to/myOutputFolder</span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 4.<span class="idiff left right">4</span> Adapting variant calling</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 4.<span class="idiff left right">5</span> Adapting variant calling</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="markdown">Sites considered for variant calling can be restricted based on the following parameters at the respective position.</span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" style="width: 35px; color: rgba(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="295" style="width: 35px; color: rgba(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">@@ -264,7 +295,8 @@ ncov_minipipe --var_call_cov 20 \</td>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-o</span> path/to/myOutputFolder</span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 4.5 Adapting variant filtering</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 4.6 Adapting variant filtering</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="markdown">Variants can be excluded, if the mean mapping quality of observed alternate alleles does not meet a given threshold (<span class="sb" style="color: #d14;">`--var_filter_mqm`</span>; default: 40).</span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="markdown">The mapping quality measures how good reads align to the respective reference genome region. Good mapping qualities are around MQ 60. </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">@@ -294,7 +326,7 @@ ncov_minipipe --var_filter_mqm 40 \</td>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-o</span> path/to/myOutputFolder</span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 4.<span class="idiff left right">6</span> Adapting consensus generation</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 4.<span class="idiff left right">7</span> Adapting consensus generation</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="markdown">When generating the consensus sequence, all positions whose read coverage is below a defined threshold can be hard-masked by N (<span class="sb" style="color: #d14;">`--cns_min_cov`</span>; default: 20). </span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="markdown">In addtion, genotypes can be adjusted meaning that variants supported by a given fraction of all reads covering the respective site are called explicitely (<span class="sb" style="color: #d14;">`--cns_gt_adjust`</span>; default: 0.9). </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">@@ -310,7 +342,7 @@ ncov_minipipe --cns_min_cov 10 \</td>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-o</span> path/to/myOutputFolder</span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 4.<span class="idiff left right">7</span> Lineage assignment </span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 4.<span class="idiff left right">8</span> Lineage assignment </span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="markdown">The generated consensus sequences can be submitted to a preliminary lineage assignment. </span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="markdown">This will run <span class="p">[</span><span class="nv" style="color: #008080;">Pangolin</span><span class="p">](</span><span class="sx" style="color: #d14;">ttps://github.com/cov-lineages/pangolin</span><span class="p">)</span> on the IUPAC consensus sequence.</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="361" style="width: 35px; color: rgba(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">@@ -329,7 +361,7 @@ ncov_minipipe --pangolin path/to/pangolin_conda_environment \</td>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 4.<span class="idiff left right">7</span>.1 Easy update or install of pangolin database</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 4.<span class="idiff left right">8</span>.1 Easy update or install of pangolin database</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="markdown">You can easily install and or update pangolin, </span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="markdown">if you have installed covpipe you should have access to the <span class="sb" style="color: #d14;">`update_pangolin`</span> script. </span>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#597ee46638e91ade71d0651e36532ab84c30fcb1"><strong>covpipe/__version__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,10 +3,9 @@ import os</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sys</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">version_info</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">MAJOR</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">MINOR</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">PATCH</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;"><span class="idiff left right">3</span></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">PATCH</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;"><span class="idiff left right">6</span></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"{MAJOR}.{MINOR}.{PATCH}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">MAJOR</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">MAJOR</span><span class="p">,</span> <span class="n" style="color: #333;">MINOR</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">MINOR</span><span class="p">,</span> <span class="n" style="color: #333;">PATCH</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PATCH</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">ADVANCED_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VERSION</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">BRANCH</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"master"</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">COMMIT</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">AHEAD</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</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">@@ -37,17 +36,6 @@ def get_more_info():</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">old_cwd</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_version</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">ADVANCED_VERSION</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">get_more_info</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">ADVANCED_VERSION</span> <span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"{vers}-{ahead}-{commit}-{branch}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">vers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">VERSION</span><span class="p">,</span> <span class="n" style="color: #333;">ahead</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">AHEAD</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">commit</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"release_commit"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">COMMIT</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">COMMIT</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">branch</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">BRANCH</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ADVANCED_VERSION</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mod_string</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">version_info</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)):</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">string</span><span class="p">.</span><span class="n" style="color: #333;">decode</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">@@ -628,8 +628,10 @@ Plotting the fragment sizes usually shows a distribution with multiple peaks. Id</td>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="plaintext"><div class=superhighimage></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="plaintext">```{r plot_fragsizes, fig.width=10, fig.height=plot.height, fig.cap="Fragment size distribution determined by the distance of reads after mapping to reference genome."}</span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="plaintext">ggplot(dt.fragsizes, aes(fragsize.abs, colour = sample, fill = sample)) +</span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="plaintext">```{r plot_fragsizes, fig.width=10, fig.height=plot.height, fig.cap="Fragment size distribution determined by the distance of reads after mapping to reference genome.", error=T}</span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="plaintext">tryCatch({</span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="plaintext"> ggplot(dt.fragsizes, aes(fragsize.abs, colour = sample, fill = sample)) +</span>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="plaintext"> geom_density() +</span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="plaintext"> facet_wrap(~sample, ncol = 4, scales = "free_y") +</span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="plaintext"> theme(axis.text.x = element_text(angle = 45, hjust = 1),</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">@@ -638,6 +640,9 @@ ggplot(dt.fragsizes, aes(fragsize.abs, colour = sample, fill = sample)) +</td>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="plaintext"> scale_x_continuous(trans = "log10") +</span>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="plaintext"> labs(title = "Fragment size histogram",</span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="plaintext"> x = "fragment size")</span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="plaintext"> }, error = function(e) {</span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="plaintext"> message("some error")</span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="plaintext"> })</span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="plaintext">```</span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#d051687e18203812decae43018b3bd6ecf28804f"><strong>covpipe/ncov_minipipe.config</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">@@ -108,6 +108,22 @@ var_filter_sap: 60</td>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="conf"><span class="n" style="color: #333;">var_filter_qual</span>: <span class="m" style="color: #099;">10</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="conf"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;">################################################################################</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># Read Filter #</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;">################################################################################</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="conf"></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># Provide the qualified quality value as a Phread score.</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># This parameter was set to 15 prior to version 3.0.4</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="conf"></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="conf"><span class="n" style="color: #333;">read_filter_qual</span>: <span class="m" style="color: #099;">20</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="conf"></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># The minimum read length. We designed the pipeline with a roughly 150 BP</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># amplicon kit in mind. If you are using it for example with </span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># one of the illumina protocols generating 75 BP reads </span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># this should be adjusted down. In the latter case 25 might be a good target</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="conf"></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="conf"><span class="n" style="color: #333;">read_filter_len</span>: <span class="m" style="color: #099;">50</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;">################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># CONSENSUS GENERATION #</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;">################################################################################</span></span>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#622a6ad92f0f17016033d2e2a3034b6709a24faf"><strong>covpipe/ncov_minipipe.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">@@ -4,23 +4,26 @@ from __future__ import print_function</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sys</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">version_info</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">datetime</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datetime</span><span class="p">,</span> <span class="n" style="color: #333;">timedelta</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">version</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></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;">argparse</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;">logging</span></span>
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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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<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;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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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;">glob</span></span>
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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;">hashlib</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span></span>
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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;">json</span></span>
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<pre style="margin: 0;">+<span id="LC12" 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="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;"> <span id="LC14" 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="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pprint</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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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;">shlex</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">strictyaml</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shlex</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC22" 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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<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;">traceback</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">urllib3</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">yaml</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="n" style="color: #333;">version</span><span class="p">.</span><span class="n" style="color: #333;">get_more_info</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># > 1. Parser Setup</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">@@ -128,6 +131,29 @@ ILLUMINA_LEGAL = "Oligonucleotide sequences © 2020 Illumina, Inc."</td>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"><span class="n" style="color: #333;">workdir_is_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"><span class="n" style="color: #333;">config_is_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"><span class="n" style="color: #333;">LEGACY_YAML_CONFIG_SCHEMA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Map</span><span class="p">(</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="p">{</span><span class="s" style="color: #d14;">"samples"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Str</span><span class="p">(),</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="s" style="color: #d14;">"output"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Str</span><span class="p">(),</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="s" style="color: #d14;">"reference"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Str</span><span class="p">(),</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="s" style="color: #d14;">"run_id"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Str</span><span class="p">(),</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="s" style="color: #d14;">"var_annotation"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Bool</span><span class="p">(),</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="s" style="color: #d14;">"cns_annotation"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Str</span><span class="p">(),</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="s" style="color: #d14;">"pangolin"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Str</span><span class="p">(),</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="s" style="color: #d14;">"primer"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Str</span><span class="p">(),</span></span>
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<td class="new_line diff-line-num new" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="s" style="color: #d14;">"adapter"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Str</span><span class="p">(),</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="s" style="color: #d14;">"var_special_interest"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Str</span><span class="p">(),</span></span>
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<td class="new_line diff-line-num new" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="s" style="color: #d14;">"var_call_cov"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="s" style="color: #d14;">"var_call_count"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="s" style="color: #d14;">"var_call_frac"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Float</span><span class="p">(),</span></span>
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<td class="new_line diff-line-num new" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="s" style="color: #d14;">"var_filter_mqm"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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<td class="new_line diff-line-num new" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="s" style="color: #d14;">"var_filter_sap"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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<td class="new_line diff-line-num new" 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">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="s" style="color: #d14;">"var_filter_qual"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Optional</span><span class="p">(</span><span class="s" style="color: #d14;">"read_filter_len"</span><span class="p">):</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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<td class="new_line diff-line-num new" 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="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Optional</span><span class="p">(</span><span class="s" style="color: #d14;">"read_filter_qual"</span><span class="p">):</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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<td class="new_line diff-line-num new" 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="s" style="color: #d14;">"cns_min_cov"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="s" style="color: #d14;">"cns_gt_adjust"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Float</span><span class="p">(),</span></span>
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<td class="new_line diff-line-num new" 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="s" style="color: #d14;">"krakenDb"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Str</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="s" style="color: #d14;">"krakenTaxID"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">()})</span></span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"></span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Settings for Default Config Schema</span></span>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"><span class="n" style="color: #333;">STRICT_YAML_CONFIG_SCHEMA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Map</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">@@ -147,6 +173,8 @@ STRICT_YAML_CONFIG_SCHEMA = strictyaml.Map(</td>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">"var_filter_mqm"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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148
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="s" style="color: #d14;">"var_filter_sap"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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149
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="s" style="color: #d14;">"var_filter_qual"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="s" style="color: #d14;">"read_filter_len"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="s" style="color: #d14;">"read_filter_qual"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="s" style="color: #d14;">"cns_min_cov"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">(),</span></span>
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="s" style="color: #d14;">"cns_gt_adjust"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Float</span><span class="p">(),</span></span>
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152
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="s" style="color: #d14;">"krakenDb"</span><span class="p">:</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">Str</span><span class="p">(),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -244,7 +272,7 @@ class ToolInfo():</td>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">response</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tool_found</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="LC274" 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="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ToolNotFoundError</span><span class="p">(</span><span class="s" style="color: #d14;">"Could not find Tool"</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="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">Tool<span class="idiff left right">Info</span>NotFoundError</span><span class="p">(</span><span class="s" style="color: #d14;">"Could not find Tool"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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248
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_version</span><span class="p">(</span><span class="bp" style="color: #999;">self</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">@@ -265,9 +293,18 @@ class ToolInfo():</td>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_snakemake_info</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ToolInfo</span><span class="p">(</span><span class="s" style="color: #d14;">"snakemake"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"snakemake"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--version"</span><span class="p">])</span> </span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">has_mamba</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC299" 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="LC300" class="line" lang="python"> <span class="n" style="color: #333;">ToolInfo</span><span class="p">(</span><span class="s" style="color: #d14;">"mamba"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"mamba"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-V"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">ret</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="LC302" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">ToolInfoNotFoundError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">snakemake</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">supress_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">snakemake</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_snakecmd</span><span class="p">(</span><span class="n" style="color: #333;">snakemake</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Snakemake Support in >Utility Section<</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">version_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"Version: {vers} - {ahead} ({commit}) {branch}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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">@@ -299,6 +336,14 @@ def main(snakemake=None,cmd=None):</td>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">DEBUG</span> </span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">debug</span> </span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">INFO</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">newer_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_newer_version</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">newer_version</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"!!There is a newer version available!!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="s" style="color: #d14;">"You are using {vers}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="s" style="color: #d14;">"The newest release is {new_vers}</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="s" style="color: #d14;">"Install it with </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">pip install covpipe --upgrade</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <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;">vers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">version</span><span class="p">.</span><span class="n" style="color: #333;">VERSION</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">new_vers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">newer_version</span><span class="p">))</span></span>
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"> <span class="s" style="color: #d14;">" ################################</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"> <span class="s" style="color: #d14;">" # #</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="363" style="width: 35px; color: rgba(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="408" style="width: 35px; color: rgba(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">@@ -363,6 +408,7 @@ def main(snakemake=None,cmd=None):</td>
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363
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#logger.exception(e)</span></span>
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409
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<pre style="margin: 0;"> <span id="LC409" 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;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Snakemake Stdout Log:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{elog}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">elog</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;">stdout</span><span class="p">))</span></span>
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Snakemake Error Log:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{elog}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">elog</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;">stderr</span><span class="p">))</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">supress_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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366
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">e</span></span>
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">QUIT_SAFE_ERROR</span><span class="p">:</span></span>
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368
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Quitting because program encountered Error"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="383" style="width: 35px; color: rgba(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="429" style="width: 35px; color: rgba(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">@@ -383,10 +429,32 @@ def main(snakemake=None,cmd=None):</td>
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383
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429
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python"> <span class="s" style="color: #d14;">"incoming+rkibioinformaticspipelines-ncov-minipipe-17578161-issue-@incoming.gitlab.com</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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384
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python"> <span class="p">)</span></span>
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385
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431
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">exception</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" 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;">supress_error</span><span class="p">:</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">exception</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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434
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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388
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435
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="python"></span>
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389
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_newer_version</span><span class="p">(</span><span class="n" style="color: #333;">proxy_par</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"http://gitlab.com/api/v4/projects/17578161/releases"</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">proxy_par</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <span class="n" style="color: #333;">proxy_par</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;">getenv</span><span class="p">(</span><span class="s" style="color: #d14;">"HTTP_PROXY"</span><span class="p">)</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">proxy_par</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">proxy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">urllib3</span><span class="p">.</span><span class="n" style="color: #333;">ProxyManager</span><span class="p">(</span><span class="n" style="color: #333;">proxy_par</span><span class="p">)</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proxy</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">(</span><span class="s" style="color: #d14;">"GET"</span><span class="p">,</span> <span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"> <span class="n" style="color: #333;">http</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">urllib3</span><span class="p">.</span><span class="n" style="color: #333;">PoolManager</span><span class="p">()</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">http</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">(</span><span class="s" style="color: #d14;">"GET"</span><span class="p">,</span> <span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json</span><span class="p">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="python"> <span class="n" style="color: #333;">new_vers_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="s" style="color: #d14;">"tag_name"</span><span class="p">].</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"> <span class="n" style="color: #333;">new_vers</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">new_vers_string</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">.</span><span class="n" style="color: #333;">VERSION</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">"v"</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">new_vers</span><span class="p">:</span> </span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_vers_string</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">json</span><span class="p">.</span><span class="n" style="color: #333;">decoder</span><span class="p">.</span><span class="n" style="color: #333;">JSONDecodeError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">retval</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># # 1. Parser Setup</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -492,6 +560,14 @@ def get_parser(version_string="Version: {vers} "</td>
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<pre style="margin: 0;"> <span id="LC560" 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 a common directory to store conda environments."</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python"> <span class="s" style="color: #d14;">" Default is using the value of the environment variable SNAKE_CONDA_PREFIX."</span></span>
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="python"> <span class="s" style="color: #d14;">" If said env var is unset, use the current working directory"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="python"> <span class="n" style="color: #333;">readgroup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">"Read Filter Options"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="python"> <span class="n" style="color: #333;">readgroup</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--read_filter_len"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p">,</span> <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>
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<pre style="margin: 0;">+<span id="LC565" 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;">"Minimum Read length. "</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"> <span class="s" style="color: #d14;">"Defaults to 50 BP "</span></span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="python"> <span class="s" style="color: #d14;">"and should be lowered when using very short read protocols"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python"> <span class="n" style="color: #333;">readgroup</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--read_filter_qual"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <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>
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<pre style="margin: 0;">+<span id="LC569" 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;">"Quality threshold for qualified quality "</span></span>
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="python"> <span class="s" style="color: #d14;">"of read as a Phredscore. Default: 20"</span><span class="p">)</span></span>
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">vargroup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">"Variation Calling in Filter Options"</span><span class="p">)</span></span>
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496
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"> <span class="n" style="color: #333;">vargroup</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--var_call_cov"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <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>
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573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Minimum coverage value to use for variant call."</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="708" style="width: 35px; color: rgba(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="784" style="width: 35px; color: rgba(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">@@ -708,7 +784,8 @@ def check_pangolin(prefix, name):</td>
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708
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784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="python"> <span class="s" style="color: #d14;">"""eval "$(conda shell.bash hook)"; {call}"""</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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709
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="python"> <span class="n" style="color: #333;">call</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">" "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">call</span><span class="p">)),</span></span>
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710
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="python"> <span class="n" style="color: #333;">shell</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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711
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="python"> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">STDOUT</span><span class="p">,</span> </span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="python"> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">STDOUT</span><span class="p">,</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="python"> <span class="n" style="color: #333;">executable</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"/bin/bash"</span><span class="p">,</span></span>
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="python"> <span class="n" style="color: #333;">universal_newlines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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713
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790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="python"> <span class="n" style="color: #333;">is_conda</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="python"> <span class="n" style="color: #333;">env_list_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">env_list</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="814" style="width: 35px; color: rgba(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">@@ -737,9 +814,10 @@ def prefix_augment(prefix):</td>
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setup_log_dir</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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738
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="python"> <span class="n" style="color: #333;">outdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span></span>
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739
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">log</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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740
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="python"> <span class="n" style="color: #333;">log_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;">join</span><span class="p">(</span><span class="n" style="color: #333;">outdir</span><span class="p">,</span> <span class="s" style="color: #d14;">"ncov-minipipe-logs"</span><span class="p">)</span> </span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="python"> <span class="n" style="color: #333;">log_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;">join</span><span class="p">(</span><span class="n" style="color: #333;">outdir</span><span class="p">,</span> <span class="s" style="color: #d14;">"results"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="python"> <span class="s" style="color: #d14;">"intermediate_data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"00_logs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"_main_log"</span><span class="p">)</span> </span>
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741
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819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="python"> <span class="n" style="color: #333;">mkdir_if_not_exists</span><span class="p">(</span><span class="n" style="color: #333;">log_prefix</span><span class="p">)</span> </span>
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742
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<pre style="margin: 0;">-<span id="LC742" class="line" lang="python"> <span class="n" style="color: #333;">logfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left">n</span>cov<span class="idiff right">-mini</span>pipe"</span> </span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="python"> <span class="n" style="color: #333;">logfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"covpipe"</span> </span>
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743
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821
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="python"> <span class="n" style="color: #333;">file_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;">join</span><span class="p">(</span><span class="n" style="color: #333;">log_prefix</span><span class="p">,</span><span class="n" style="color: #333;">logfile</span><span class="p">)</span></span>
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744
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822
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">file_prefix</span> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".log"</span><span class="p">):</span></span>
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745
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823
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="python"> <span class="n" style="color: #333;">logfile</span><span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{_file}_{timestamp}.log"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1069" style="width: 35px; color: rgba(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">@@ -991,6 +1069,7 @@ def build_config_from_args(args):</td>
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991
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1069
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<pre style="margin: 0;"> <span id="LC1069" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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992
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1070
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<pre style="margin: 0;"> <span id="LC1070" class="line" lang="python"> <span class="n" style="color: #333;">config_location</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span></span>
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993
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1071
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<pre style="margin: 0;"> <span id="LC1071" class="line" lang="python"> <span class="n" style="color: #333;">schema</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">STRICT_YAML_CONFIG_SCHEMA</span></span>
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1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="python"> <span class="n" style="color: #333;">fallbackSchema</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LEGACY_YAML_CONFIG_SCHEMA</span> </span>
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994
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1073
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<pre style="margin: 0;"> <span id="LC1073" class="line" lang="python"> <span class="n" style="color: #333;">found_config</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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995
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1074
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<pre style="margin: 0;"> <span id="LC1074" class="line" lang="python"> <span class="n" style="color: #333;">sample_conf_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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996
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1075
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<pre style="margin: 0;"> <span id="LC1075" class="line" lang="python"> <span class="n" style="color: #333;">config_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1078" style="width: 35px; color: rgba(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">@@ -999,13 +1078,19 @@ def build_config_from_args(args):</td>
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999
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1078
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<pre style="margin: 0;"> <span id="LC1078" 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;">DEFAULT_CONFIG_TEMPLATE</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">conf_fh</span><span class="p">:</span></span>
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1000
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1079
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1001
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1080
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<pre style="margin: 0;"> <span id="LC1080" 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;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">conf_fh</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(),</span> <span class="n" style="color: #333;">schema</span><span class="p">)</span></span>
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1002
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">exceptions</span><span class="p">.</span><span class="n" style="color: #333;">YAMLValidationError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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1003
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="python"> <span class="n" style="color: #333;">context</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;">args</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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1004
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<pre style="margin: 0;">-<span id="LC1004" 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 in Config:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{before}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC1005" class="line" lang="python"> <span class="s" style="color: #d14;">" #vvvv Error Line vvvv#{lines}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">context</span><span class="p">.</span><span class="n" style="color: #333;">lines</span><span class="p">(),</span></span>
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1006
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="python"> <span class="n" style="color: #333;">before</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">context</span><span class="p">.</span><span class="n" style="color: #333;">lines_before</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">)))</span></span>
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1007
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">exception</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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1008
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<pre style="margin: 0;">-<span id="LC1008" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">e</span> </span>
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1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">exceptions</span><span class="p">.</span><span class="n" style="color: #333;">YAMLValidationError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">og_e</span><span class="p">:</span></span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="python"> <span class="n" style="color: #333;">conf_fh</span><span class="p">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1084
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<pre style="margin: 0;">+<span id="LC1084" 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;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">conf_fh</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(),</span> <span class="n" style="color: #333;">fallbackSchema</span><span class="p">)</span> </span>
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">strictyaml</span><span class="p">.</span><span class="n" style="color: #333;">exceptions</span><span class="p">.</span><span class="n" style="color: #333;">YAMLValidationError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="python"> <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">og_e</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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1087
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<pre style="margin: 0;">+<span id="LC1087" 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>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="python"> <span class="s" style="color: #d14;">"Error in Config:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{before}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="python"> <span class="s" style="color: #d14;">" #vvvv Error Line vvvv#{lines}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">context</span><span class="p">.</span><span class="n" style="color: #333;">lines</span><span class="p">(),</span></span>
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1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="python"> <span class="n" style="color: #333;">before</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">context</span><span class="p">.</span><span class="n" style="color: #333;">lines_before</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">)))</span></span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">exception</span><span class="p">(</span><span class="n" style="color: #333;">og_e</span><span class="p">)</span></span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">og_e</span> </span>
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1009
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<td class="new_line diff-line-num" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1094
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<pre style="margin: 0;"> <span id="LC1094" class="line" lang="python"> <span class="n" style="color: #333;">sample_conf_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">"samples"</span><span class="p">].</span><span class="n" style="color: #333;">data</span></span>
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1010
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1095
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<pre style="margin: 0;"> <span id="LC1095" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check user provided</span></span>
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1011
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1096
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<pre style="margin: 0;"> <span id="LC1096" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">conf</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1146,6 +1231,9 @@ def augment_config_with_args(args, config):</td>
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1146
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1231
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<pre style="margin: 0;"> <span id="LC1231" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">"var_filter_mqm"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">var_filter_mqm</span></span>
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1147
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1232
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<pre style="margin: 0;"> <span id="LC1232" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">"var_filter_sap"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">var_filter_sap</span></span>
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1148
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1233
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<pre style="margin: 0;"> <span id="LC1233" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">"var_filter_qual"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">var_filter_qual</span></span>
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1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="python"> </span>
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1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">"read_filter_len"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">read_filter_len</span></span>
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1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">"read_filter_qual"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">read_filter_qual</span></span>
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1149
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1237
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<pre style="margin: 0;"> <span id="LC1237" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">"cns_min_cov"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cns_min_cov</span></span>
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1150
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1238
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<pre style="margin: 0;"> <span id="LC1238" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">"cns_gt_adjust"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cns_gt_adjust</span></span>
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1151
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1239
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<pre style="margin: 0;"> <span id="LC1239" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">var_special_interest</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1532" style="width: 35px; color: rgba(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="1620" style="width: 35px; color: rgba(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">@@ -1532,10 +1620,13 @@ def prep_snake_call(args, rerun_dict, snake_cmd, name="Change"):</td>
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1532
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1620
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<pre style="margin: 0;"> <span id="LC1620" class="line" lang="python"> <span class="n" style="color: #333;">outs</span><span class="p">,</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prep_proc</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()</span></span>
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1533
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1621
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<pre style="margin: 0;"> <span id="LC1621" class="line" lang="python"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prep_proc</span><span class="p">.</span><span class="n" style="color: #333;">wait</span><span class="p">()</span></span>
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1534
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1622
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<pre style="margin: 0;"> <span id="LC1622" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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1535
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<pre style="margin: 0;">-<span id="LC1535" class="line" lang="python"> <span class="n" style="color: #333;">handle_snakemake_syntax_error</span><span class="p">(</span></span>
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1536
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<pre style="margin: 0;">-<span id="LC1536" class="line" lang="python"> <span class="s" style="color: #d14;">"{err}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{out}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mod_string</span><span class="p">(</span><span class="n" style="color: #333;">err</span><span class="p">),</span></span>
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1537
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<pre style="margin: 0;">-<span id="LC1537" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mod_string</span><span class="p">(</span><span class="n" style="color: #333;">outs</span><span class="p">)),</span></span>
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1538
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<pre style="margin: 0;">-<span id="LC1538" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">blame</span><span class="p">)</span></span>
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1623
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<pre style="margin: 0;">+<span id="LC1623" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1624
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<pre style="margin: 0;">+<span id="LC1624" class="line" lang="python"> <span class="n" style="color: #333;">handle_snakemake_syntax_error</span><span class="p">(</span></span>
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1625
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<pre style="margin: 0;">+<span id="LC1625" class="line" lang="python"> <span class="s" style="color: #d14;">"{err}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{out}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mod_string</span><span class="p">(</span><span class="n" style="color: #333;">err</span><span class="p">),</span></span>
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1626
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<pre style="margin: 0;">+<span id="LC1626" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mod_string</span><span class="p">(</span><span class="n" style="color: #333;">outs</span><span class="p">)),</span></span>
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1627
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<pre style="margin: 0;">+<span id="LC1627" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">blame</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1628
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<pre style="margin: 0;">+<span id="LC1628" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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1629
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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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1539
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1630
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<pre style="margin: 0;"> <span id="LC1630" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SNAKEMAKE_RUN_ERROR</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">call</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">' '</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">snake_cmd</span><span class="p">),</span></span>
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1540
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1631
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<pre style="margin: 0;"> <span id="LC1631" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mod_string</span><span class="p">(</span><span class="n" style="color: #333;">outs</span><span class="p">),</span></span>
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1541
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1632
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<pre style="margin: 0;"> <span id="LC1632" class="line" lang="python"> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mod_string</span><span class="p">(</span><span class="n" style="color: #333;">err</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1564" style="width: 35px; color: rgba(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="1655" style="width: 35px; color: rgba(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">@@ -1564,13 +1655,16 @@ def real_snake_call(args, unknown_args, conf, samp_conf, rerun_list):</td>
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1564
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1655
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<pre style="margin: 0;"> <span id="LC1655" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rerun_list</span><span class="p">:</span></span>
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1565
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1656
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<pre style="margin: 0;"> <span id="LC1656" class="line" lang="python"> <span class="n" style="color: #333;">rerun_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"-R"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rerun_list</span></span>
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1566
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1657
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<pre style="margin: 0;"> <span id="LC1657" class="line" lang="python"> <span class="n" style="color: #333;">conda_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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1658
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<pre style="margin: 0;">+<span id="LC1658" class="line" lang="python"> <span class="n" style="color: #333;">conda_frontend</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"--conda-frontend"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mamba"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">has_mamba</span><span class="p">()</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"conda"</span><span class="p">]</span> </span>
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1567
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1659
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<pre style="margin: 0;"> <span id="LC1659" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">conda_prefix</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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1568
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1660
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<pre style="margin: 0;"> <span id="LC1660" class="line" lang="python"> <span class="n" style="color: #333;">conda_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"-d"</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span></span>
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1569
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1661
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<pre style="margin: 0;"> <span id="LC1661" class="line" lang="python"> <span class="s" style="color: #d14;">'--conda-prefix'</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">conda_prefix</span><span class="p">]</span></span>
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1570
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1662
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<pre style="margin: 0;"> <span id="LC1662" class="line" lang="python"> <span class="n" style="color: #333;">snake_cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">BASIC_SNAKE_CALL</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span> <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cpus</span><span class="p">)</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="s" style="color: #d14;">"--configfile"</span><span class="p">,</span> <span class="n" style="color: #333;">conf</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>
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1571
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<td class="new_line diff-line-num" data-linenumber="1663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1663
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<pre style="margin: 0;"> <span id="LC1663" class="line" lang="python"> <span class="n" style="color: #333;">rerun_list</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">unknown_args</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="s" style="color: #d14;">"--use-conda"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">conda_prefix</span><span class="p">)</span></span>
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1664
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<pre style="margin: 0;">+<span id="LC1664" class="line" lang="python"> <span class="n" style="color: #333;">snake_cmd</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">conda_frontend</span><span class="p">)</span></span>
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1572
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1665
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<pre style="margin: 0;"> <span id="LC1665" class="line" lang="python"> <span class="n" style="color: #333;">short_snake_cmd</span> <span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">BASIC_SNAKE_CALL</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span> <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cpus</span><span class="p">)</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="s" style="color: #d14;">"--configfile"</span><span class="p">,</span> <span class="n" style="color: #333;">conf</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>
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1573
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1666
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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="python"> <span class="n" style="color: #333;">unknown_args</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="s" style="color: #d14;">"--use-conda"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">conda_prefix</span><span class="p">)</span></span>
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1667
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<pre style="margin: 0;">+<span id="LC1667" class="line" lang="python"> <span class="n" style="color: #333;">short_snake_cmd</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">conda_frontend</span><span class="p">)</span></span>
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1574
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1668
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<pre style="margin: 0;"> <span id="LC1668" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">unknown_args</span><span class="p">:</span></span>
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1575
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1669
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<pre style="margin: 0;"> <span id="LC1669" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Arguments not known are being appended to the snakemake call.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1576
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1670
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<pre style="margin: 0;"> <span id="LC1670" class="line" lang="python"> <span class="s" style="color: #d14;">"Please refer to the snakemake help for issues encountered.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1648" style="width: 35px; color: rgba(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="1742" style="width: 35px; color: rgba(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">@@ -1648,11 +1742,11 @@ def handle_snakemake_syntax_error(string, blame):</td>
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1648
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1742
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<pre style="margin: 0;"> <span id="LC1742" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">blame</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">match</span><span class="p">:</span></span>
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1649
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1743
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<pre style="margin: 0;"> <span id="LC1743" class="line" lang="python"> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">match</span><span class="p">.</span><span class="n" style="color: #333;">groupdict</span><span class="p">()</span></span>
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1650
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1744
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<pre style="margin: 0;"> <span id="LC1744" class="line" lang="python"> <span class="n" style="color: #333;">lnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">match</span><span class="p">[</span><span class="s" style="color: #d14;">"line"</span><span class="p">])</span></span>
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1651
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<pre style="margin: 0;">-<span id="LC1651" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;">lnum</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">19</span></span><span class="p"><span class="idiff right">:</span></span></span>
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1652
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<pre style="margin: 0;">-<span id="LC1652" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">bounds</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"1,20"</span></span></span>
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1653
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<pre style="margin: 0;">-<span id="LC1653" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">else</span></span><span class="p"><span class="idiff right">:</span></span></span>
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1654
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<pre style="margin: 0;">-<span id="LC1654" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{start},{end}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lnum</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1655" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">lnum</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">10</span></span><span class="p">)</span></span>
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1745
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<pre style="margin: 0;">+<span id="LC1745" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">max_</span>lnum</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">lnum</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">10</span></span></span>
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1746
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<pre style="margin: 0;">+<span id="LC1746" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">with</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">match</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"file"</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"r"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fh</span></span><span class="p"><span class="idiff right">:</span></span></span>
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1747
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<pre style="margin: 0;">+<span id="LC1747" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">max_lnum</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fh</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">readlines</span></span><span class="p"><span class="idiff right">())</span></span></span>
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<pre style="margin: 0;">+<span id="LC1748" class="line" lang="python"> <span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{start},{end}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left">max</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">lnum</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">),</span></span></span>
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<pre style="margin: 0;">+<span id="LC1749" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">end</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">min</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lnum</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">10</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_lnum</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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1656
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1750
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<pre style="margin: 0;"> <span id="LC1750" class="line" lang="python"> <span class="n" style="color: #333;">old_cwd</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;">getcwd</span><span class="p">()</span></span>
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1657
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1751
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<pre style="margin: 0;"> <span id="LC1751" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1658
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1752
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<pre style="margin: 0;"> <span id="LC1752" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">SOURCE_DIR</span><span class="p">)</span></span>
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<li id="838ab6c5a4748a40ff545721edd87ac5d144dd0f">
<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#838ab6c5a4748a40ff545721edd87ac5d144dd0f"><strong>covpipe/ncov_minipipe.snake</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">@@ -13,7 +13,7 @@ import os</td>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">import pprint</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">import sys</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">import yaml</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"><span class="idiff left right">import __version__ as _vers_</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"># DEBUGGING</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">## use as DEBUG(variable) for debugging at runtime</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +21,12 @@ pp = pprint.PrettyPrinter(indent=4)</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">DEBUG = pp.pprint</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">def default_if_not(key, _dict, default):</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> try:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> return _dict[key]</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> except KeyError:</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> return default</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"># INPUT CHECK</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">## preparing checks</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">def checkConfigKey(key, config):</span>
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<td class="diff-line-num unfold js-unfold old_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="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">@@ -140,6 +146,10 @@ VAR_FILTER_MQM = config['var_filter_mqm']</td>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="plaintext">VAR_FILTER_SAP = config['var_filter_sap']</span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext">VAR_FILTER_QUAL = config['var_filter_qual']</span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">## read filtering</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">READ_FILTER_QUAL = default_if_not("read_filter_qual", config, 20)</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">READ_FILTER_LEN = default_if_not("read_filter_len", config, 50)</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext">## consensus generation</span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext">CNS_MIN_COV = config['cns_min_cov']</span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext">CNS_GT_ADJUST = config["cns_gt_adjust"] if checkConfigKey('cns_gt_adjust', config) else None</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="210" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -210,6 +220,7 @@ def input_all(wildcards):</td>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext"> if PANGOLIN:</span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="plaintext"> for sample in SAMPLES:</span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="plaintext"> files.append(os.path.join(DATAFOLDER["lineages"], sample, sample + ".lineage.txt"))</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"> files.append(os.path.join(DATAFOLDER["lineages"], "all_samples.lineage.txt"))</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"> ## variant annotation</span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="plaintext"> if VAR_VOI != "no valid vcf input provided":</span>
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<li id="80f2e49a40c26133b9b6bcdfcf08efdfa2247a37">
<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#80f2e49a40c26133b9b6bcdfcf08efdfa2247a37"><strong>covpipe/rules/assign_lineage.smk</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">@@ -18,3 +18,15 @@ rule assign_lineage:</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> conda activate {params.pangolin_env} &> {log}</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> pangolin --outdir {params.dir} --outfile {params.fname} --tempdir {params.dir} --threads {threads} {input.fasta} &>> {log}</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> """</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">rule fuse_lineage:</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> input:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> expand(os.path.join(DATAFOLDER["lineages"], "{sample}",</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> "{sample}.lineage.txt"), sample=SAMPLES)</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> output:</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> os.path.join(DATAFOLDER["lineages"], "all_samples.lineage.txt")</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> shell:</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> r"""</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> head -n1 {input[0]} > {output}</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> ls -1 {input} | xargs -I '{{}}' tail -n +2 {{}} >> {output}</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> """</span></pre>
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<li id="491269433cdc279dd18f2793a30f11bf9abf9a55">
<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#491269433cdc279dd18f2793a30f11bf9abf9a55"><strong>covpipe/rules/classify_reads.smk</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,4 +29,5 @@ rule classifyReads:</td>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> --report {output.kraken_report} \</span>
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30
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> --gzip-compressed \</span>
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31
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> {input.PE1} {input.PE2} ) 2> {log}</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> #echo > {output.PE1} ; echo > {output.PE2} </span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> """</span></pre>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#d775516cdb3f3ec1ad8cb5e542e7cab3c007df47"><strong>covpipe/rules/get_version.smk</strong></a>
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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">@@ -8,10 +8,8 @@ rule getVersion:</td>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> sd = srcdir(".")</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> log:</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> os.path.join(DATAFOLDER["logs"], "version", "git.repository.version.log")</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> run:</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> with open(output[0],"w") as out_fh:</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> print(_vers_.get_version(), file=out_fh)</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"># r"""0</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># cd {params.sd};</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"># git describe 1> {output} 2> {log} || echo 'unknown_version' 1> {output} 2> {log}</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"># """</span></pre>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> shell:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> r"""</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> cd {params.sd};</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> git describe 1> {output} 2> {log} || echo 'unknown_version' 1> {output} 2> {log}</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> """</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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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#dca120fe48a8f069b9b95e3209aa9f51daccc7d9"><strong>covpipe/rules/trim_reads.smk</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">@@ -19,26 +19,40 @@ rule trimReads:</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> log:</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> os.path.join(DATAFOLDER["logs"], "trimming", "{sample}.log")</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> params:</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> adapters = "--adapter_fasta " + ADAPTERS if ADAPTERS else ""</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> adapters = "--adapter_fasta " + ADAPTERS if ADAPTERS else "",</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> reqlen = ("--length_required {}".format(READ_FILTER_LEN) </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> if READ_FILTER_LEN != -1</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> else ""),</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> qualfilter = "--qualified_quality_phred {}".format(READ_FILTER_QUAL) </span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> conda:</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> "../envs/fastp.yaml"</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> threads:</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> 1</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> shell:</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> r"""</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> ( fastp \</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> --in1 {input[0]} \</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> --out1 {output.PE1} \</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> --in2 {input[1]} \</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> --out2 {output.PE2} \</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> --unpaired1 {output.SE1} \</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> --unpaired2 {output.SE2} \</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> --json {output.json} \</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> --html {output.html} \</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> </span>
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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"> conda list -p $CONDA_PREFIX | grep fastp</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> set -x</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> fastp \</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> --in1 {input[0]} \</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> --out1 {output.PE1} \</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> --in2 {input[1]} \</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> --out2 {output.PE2} \</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> --unpaired1 {output.SE1} \</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> --unpaired2 {output.SE2} \</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> --json {output.json} \</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> --html {output.html} \</span>
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38
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> {params.adapters} \</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> <span class="idiff left">--</span>qual<span class="idiff">i</span>fi<span class="idiff right">ed_quality_phred 15</span> \</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> <span class="idiff left right">--length_required 50</span> \</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> <span class="idiff left">{params.</span>qualfi<span class="idiff right">lter}</span> \</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> <span class="idiff left right">{params.reqlen}</span> \</span>
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41
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> --low_complexity_filter \</span>
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42
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> --overrepresentation_analysis \</span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> --thread {threads} ) &> {log}</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> --thread {threads} || {{</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> ret=$?</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> cp {log} $( sed -E 's/(.+).log/\1.err.log/' <<< {log} )</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> exit $ret</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> }} </span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> set +x </span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> ) &> {log}</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> """</span></pre>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#4b2465b2029aef2dcee63d208c5b8609d5678dbd"><strong>covpipe_env.yaml</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">@@ -4,7 +4,7 @@ channels:</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda-forge</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">defaults</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">dependencies</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">snakemake>=5.26</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">snakemake<span class="idiff left"> </span>>=5.26<span class="idiff right">, <6.1.0</span></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pysam</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">biopython</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">strictyaml</span></span>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#3f60363c5cb77eeb90e9a3f00e6ab04919814822"><strong>covpipe_tools/primerbed2bedpe.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.0.1"</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">snakemake</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_argparser</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;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from_snakemake</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">snakemake</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">reformat_bedpe</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_argparser</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="s" style="color: #d14;">"bed2bedpe"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">"Tool to quickly transform a primer bed file to a bedpe</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">"It uses the naming sheme of primers to asign them.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> "</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">"amp1(_LEFT)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">"amp2(_RIGHT)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">"{_LEFT|_RIGHT} are the default identifiers the tool looks for. "</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">"When multiple pairs are possible for an amplicon,"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">" the cartesian product is used.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">"Multiple paired end records with the same id will be outputted</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">" and the score field will be incremented for each duplicate"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"primer_bed"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"bed file with primer positions"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--forward_identifier"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"_LEFT"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" 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;">"identifier used to identify left amplicon primer."</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">" default: _LEFT"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--reverse_identifier"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"_RIGHT"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC36" 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;">"identifier used to identify right amplicon primer."</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">" default: _RIGHT"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-o"</span><span class="p">,</span><span class="s" style="color: #d14;">"--output"</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"primer.bedpe"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC39" 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;">"Output file name. default: primer.bedpe"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">from_snakemake</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">snakemake</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cmd</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reformat_bedpe</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">bed_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">primer_bed</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">for_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">forward_identifier</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">rev_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">reverse_identifier</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">bed_file</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">,</span><span class="s" style="color: #d14;">"start"</span><span class="p">,</span><span class="s" style="color: #d14;">"end"</span><span class="p">,</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span><span class="s" style="color: #d14;">"score"</span><span class="p">,</span> <span class="s" style="color: #d14;">"strand"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</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="n" style="color: #333;">for_id</span><span class="p">,</span><span class="n" style="color: #333;">rev_id</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">func</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">split_pattern</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">pattern</span><span class="p">,</span> <span class="n" style="color: #333;">for_id</span><span class="p">,</span> <span class="n" style="color: #333;">rev_id</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">parse_bed_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">concat</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">bed</span><span class="p">.</span><span class="n" style="color: #333;">iloc</span><span class="p">[:,</span><span class="mi" style="color: #099;">3</span><span class="p">].</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">)))</span> </span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">parse_bed_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">bed</span><span class="p">,</span> <span class="n" style="color: #333;">parse_bed_ids</span><span class="p">,</span><span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"left"</span><span class="p">,</span> <span class="n" style="color: #333;">left_on</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="n" style="color: #333;">right_on</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"key"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" 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;">outfile</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">o_fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group_id</span><span class="p">,</span> <span class="n" style="color: #333;">keys</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parse_bed_ids</span><span class="p">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">"id"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">l_data</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">r_data</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">keys</span><span class="p">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">"reverse"</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,(</span><span class="n" style="color: #333;">li</span><span class="p">,</span><span class="n" style="color: #333;">ri</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">([(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">l_data</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">r_data</span><span class="p">))]):</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">l_temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l_data</span><span class="p">.</span><span class="n" style="color: #333;">iloc</span><span class="p">[</span><span class="n" style="color: #333;">li</span><span class="p">,:]</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">r_temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r_data</span><span class="p">.</span><span class="n" style="color: #333;">iloc</span><span class="p">[</span><span class="n" style="color: #333;">ri</span><span class="p">,:]</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">l_temp</span><span class="p">[[</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">,</span><span class="s" style="color: #d14;">"start"</span><span class="p">,</span><span class="s" style="color: #d14;">"end"</span><span class="p">]]))</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">r_temp</span><span class="p">[[</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">,</span><span class="s" style="color: #d14;">"start"</span><span class="p">,</span><span class="s" style="color: #d14;">"end"</span><span class="p">]]))</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">group_id</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">l_temp</span><span class="p">[</span><span class="s" style="color: #d14;">"strand"</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">r_temp</span><span class="p">[</span><span class="s" style="color: #d14;">"strand"</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">o_fh</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">split_pattern</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">pattern</span><span class="p">,</span> <span class="n" style="color: #333;">for_id</span><span class="p">,</span> <span class="n" style="color: #333;">rev_id</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"key"</span><span class="p">:</span><span class="n" style="color: #333;">val</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">"id"</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">"reverse"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">"orient_id"</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="s" style="color: #d14;">"add"</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">val</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;">if</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="s" style="color: #d14;">"id"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="p">.</span><span class="n" style="color: #333;">groups</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="s" style="color: #d14;">"reverse"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="p">.</span><span class="n" style="color: #333;">groups</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rev_id</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="s" style="color: #d14;">"orient_id"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="p">.</span><span class="n" style="color: #333;">groups</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="s" style="color: #d14;">"add"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="p">.</span><span class="n" style="color: #333;">groups</span><span class="p">()[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="s" style="color: #d14;">"key"</span><span class="p">]])</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#ee30b68dd2215790f03019a13c78092a44587207"><strong>covpipe_tools/update_pangolin.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">@@ -50,7 +50,7 @@ def main(CMD=None, snakemake=None):</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC51" 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="LC52" 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;">args</span><span class="p">.</span><span class="n" style="color: #333;">use_conda_default</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">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;">join</span><span class="p">(</span><span class="n" style="color: #333;">covpipe_default_location</span><span class="p">,</span> <span class="n" style="color: #333;">args</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="LC53" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">prefix</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff right"> </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;">join</span><span class="p">(</span><span class="n" style="color: #333;">covpipe_default_location</span><span class="p">,</span> <span class="n" style="color: #333;">args</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="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Checking Environment Availability:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">tool_availability</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">has_conda</span><span class="p">,</span> <span class="n" style="color: #333;">parsed_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">found_pangolin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -202,6 +202,10 @@ def git_manual_update(prefix):</td>
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">CalledProcessError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> </span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">run_unsafe_command_in_pangolin</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="s" style="color: #d14;">"python -m pip install {git} --upgrade"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">git</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"git+https://github.com/cov-lineages/constellations.git"</span><span class="p">))</span></span>
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205
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Updating PangoLearn..."</span><span class="p">)</span></span>
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206
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">run_unsafe_command_in_pangolin</span><span class="p">(</span></span>
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207
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">prefix</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">@@ -218,7 +222,7 @@ def run_unsafe_command_in_pangolin(prefix, cmd):</td>
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218
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pushd</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">):</span></span>
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219
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">(</span></span>
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220
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="s" style="color: #d14;">""" eval "$(conda shell.bash hook)"; conda activate ./ && {cmd} && conda deactivate"""</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cmd</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">shell</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="LC225" class="line" lang="python"> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">executable</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">'/bin/bash'</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#97d42055d8a8ae104887701fdda7934b652e6192"><strong>ncov_minipipe.conda.setup/setup_env.sh</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,7 +49,7 @@ update_conda_or_install(){</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell"> <span class="nv" style="color: #008080;">$CONDA_FRONTEND</span> <span class="nb" style="color: #0086b3;">install</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"> <span class="nt" style="color: #000080;">-c</span> conda-forge <span class="nt" style="color: #000080;">-c</span> bioconda <span class="nt" style="color: #000080;">-c</span> defaults <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"> <span class="s2" style="color: #d14;">"python>=3.6.0"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="shell"> <span class="s2" style="color: #d14;">"snakemake>=5.26"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"> <span class="s2" style="color: #d14;">"snakemake>=5.26<span class="idiff left right">,<6.1</span>"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="shell"> <span class="s2" style="color: #d14;">"pysam"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="shell"> <span class="s2" style="color: #d14;">"biopython"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="shell"> strictyaml <span class="se" style="color: #d14;">\</span></span>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">tests_require</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"pytest"</span><span class="p">,</span><span class="s" style="color: #d14;">"PyYAML"</span><span class="p">,</span> <span class="s" style="color: #d14;">"pandas"</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">"snakemake>5.26"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">"snakemake<span class="idiff left"> </span>>5.26<span class="idiff right">, <7</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"strictyaml"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"PyYAML"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"biopython"</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">@@ -27,6 +27,7 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">'covpipe = covpipe.ncov_minipipe:main'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">'ncov_minipipe = covpipe.ncov_minipipe:main'</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">'create_bedpe = covpipe_tools.create_bedpe:main'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">'bed2bedpe = covpipe_tools.primerbed2bedpe:main'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">'update_pangolin = covpipe_tools.update_pangolin:main'</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="p">]},</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">include_package_data</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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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#7cc23430d3e061a3235f9c707657bbeea004459f"><strong>tests/TestData/GEN_SAMPLES/mixture.csv</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">@@ -5,3 +5,4 @@ Sample_4_r150_MSv3;WUHAN1_RAW_ALLVARS_50X_r159_MSv3;WUHAN1_NOVAR_MSv3_RAW_50X_L1</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Sample_5_r150_MSv3;WUHAN1_RAW_ALLVARS_50X_r159_MSv3;WUHAN1_NOVAR_MSv3_RAW_50X_L150;.30</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Sample_6_r150_MSv3;WUHAN1_RAW_ALLVARS_50X_r159_MSv3;WUHAN1_NOVAR_MSv3_RAW_50X_L150;.20</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Sample_7_r150_MSv3;Sample_2_r150_MSv3;ColdCorona_MSv3_RAW_50X_L150;.89</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Sample_8_r150_MSv3;ColdCorona_MSv3_RAW_50X_L150;ColdRhino_MSv3_RAW_50X_L150;.50</span></pre>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250#1ae8c96e8d5c628787ec4ee9c13d9c7baf1b2d4a"><strong>tests/quicktest.sh</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">@@ -56,6 +56,7 @@ stop_setup(){</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell">main<span class="o" style="font-weight: 600;">(){</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">PROXY</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">kraken</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"> <span class="nv" style="color: #008080;">snake_args</span><span class="o" style="font-weight: 600;">=(</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">)</span> </span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">covpipe_package_exists</span><span class="o" style="font-weight: 600;">=</span>0</span>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span>conda list | <span class="nb" style="color: #0086b3;">grep </span>covpipe <span class="p">;</span> <span class="k" style="font-weight: 600;">then</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">@@ -68,7 +69,7 @@ main(){</td>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell"></span>
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70
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">skipconda</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">covpipe_package_exists</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="shell"> <span class="k" style="font-weight: 600;">while </span><span class="nb" style="color: #0086b3;">getopts</span> <span class="s2" style="color: #d14;">"p:sn"</span> flag<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"> <span class="k" style="font-weight: 600;">while </span><span class="nb" style="color: #0086b3;">getopts</span> <span class="s2" style="color: #d14;">"p:sn<span class="idiff left right">k</span>"</span> flag<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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72
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"><span class="k" style="font-weight: 600;"> case</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$flag</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">in </span></span>
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73
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>p<span class="p">)</span> <span class="nv" style="color: #008080;">PROXY</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OPTARG</span></span>
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="shell"> <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">@@ -76,6 +77,8 @@ main(){</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"> n<span class="p">)</span> <span class="nv" style="color: #008080;">snake_args</span><span class="o" style="font-weight: 600;">=(</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">snake_args</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"-n"</span><span class="o" style="font-weight: 600;">)</span></span>
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78
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="shell"> <span class="p">;;</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"> k<span class="p">)</span> <span class="nv" style="color: #008080;">kraken</span><span class="o" style="font-weight: 600;">=</span>1</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"> <span class="p">;;</span></span>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span> </span>
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80
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span></span>
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81
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">shift</span> <span class="k" style="font-weight: 600;">$((</span> <span class="nv" style="color: #008080;">$OPTIND</span> <span class="o" style="font-weight: 600;">-</span> <span class="m" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">))</span> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -117,12 +120,27 @@ run_tests(){</td>
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117
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="shell"> activate_conda <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TESTENV</span><span class="s2" style="color: #d14;">"</span></span>
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118
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="shell"> <span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">';'</span> <span class="nb" style="color: #0086b3;">read</span> <span class="nt" style="color: #000080;">-a</span> READS <span class="o" style="font-weight: 600;"><<<</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$GEN_SCR</span><span class="s2" style="color: #d14;">"</span> Sample_7 gen<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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119
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="shell"> <span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">';'</span> <span class="nb" style="color: #0086b3;">read</span> <span class="nt" style="color: #000080;">-a</span> READS_TEST02 <span class="o" style="font-weight: 600;"><<<</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$GEN_SCR</span><span class="s2" style="color: #d14;">"</span> Sample_6 gen<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="shell"> <span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">';'</span> <span class="nb" style="color: #0086b3;">read</span> <span class="nt" style="color: #000080;">-a</span> READS_TEST04 <span class="o" style="font-weight: 600;"><<<</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$GEN_SCR</span><span class="s2" style="color: #d14;">"</span> Sample_8 gen<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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120
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<td class="new_line diff-line-num" 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">
124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">REF</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span> <span class="nv" style="color: #008080;">http_proxy</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$http_proxy</span> <span class="nv" style="color: #008080;">$REF_SCR</span> SarsCov2Wuhan1 gen<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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121
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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">VCF</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nv" style="color: #008080;">$VCF_SCR</span> VCF_ALL_VARS gen<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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122
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">adapter</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GIT_ROOT</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/adapter.fasta"</span></span>
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123
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="shell"> deactivate_conda</span>
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124
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">testid</span><span class="o" style="font-weight: 600;">=</span>test01</span>
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125
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<td class="new_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$testid</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="shell"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$covpipe_package_exists</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span></span>
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<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>activate_conda <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$PROGENV</span><span class="s2" style="color: #d14;">"</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#test01</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="shell"> test02 </span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="shell"> test03</span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$kraken</span> <span class="nt" style="color: #000080;">-eq</span> 1 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>test04</span>
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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="new_line diff-line-num new" 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">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>deactivate_conda</span>
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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="shell">test01<span class="o" style="font-weight: 600;">(){</span></span>
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">testpath</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">realpath</span> <span class="nv" style="color: #008080;">$testid</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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127
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">testsampleconf</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">testpath</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/sample.conf.yaml"</span></span>
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">testconf</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">testpath</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/ncov_minipipe.config"</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">@@ -145,13 +163,13 @@ run_tests(){</td>
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="shell"> <span class="s2" style="color: #d14;">" read2: </span><span class="se" style="color: #d14;">\"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">READS</span><span class="p">[1]</span><span class="k" style="font-weight: 600;">}</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\</span></span>
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="shell"> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$testsampleconf</span><span class="s2" style="color: #d14;">"</span></span>
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147
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="shell"></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="shell"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$covpipe_package_exists</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-eq</span></span><span class="idiff"> 0 </span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">then </span></span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="shell"><span class="k" style="font-weight: 600;"> <span class="idiff left"> </span></span><span class="idiff">activate_conda </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$PROGENV</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="shell"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">fi</span></span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#echo ncov_minipipe --conf "$testconf" -o $testid \</span></span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="shell"><span class="idiff left"> </span><span class="c" style="color: #998; font-style: italic;"><span class="idiff right"># --conda_prefix "${TESTENVDIR}" --blame</span></span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="shell"><span class="idiff left"> </span><span class="c" style="color: #998; font-style: italic;"><span class="idiff right">#ncov_minipipe --conf "$testconf" -o $testid \</span></span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="shell"><span class="idiff left"> </span><span class="c" style="color: #998; font-style: italic;"><span class="idiff right"># --conda_prefix "${TESTENVDIR}" --blame ${snake_args[@]}</span></span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="shell"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo </span></span><span class="idiff">ncov_minipipe </span><span class="nt" style="color: #000080;"><span class="idiff">--conf</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$testconf</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$testid</span></span><span class="idiff"> </span><span class="se" style="color: #d14;"><span class="idiff right">\</span></span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="shell"> <span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff">--conda_prefix</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">TESTENVDIR</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff right">--blame</span></span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="shell"><span class="idiff left"> ncov_minipipe </span><span class="nt" style="color: #000080;"><span class="idiff">--conf</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$testconf</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$testid</span></span><span class="idiff"> </span><span class="se" style="color: #d14;"><span class="idiff right">\</span></span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="shell"> <span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff">--conda_prefix</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">TESTENVDIR</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">--blame</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">snake_args</span></span><span class="p"><span class="idiff">[@]</span></span><span class="k" style="font-weight: 600;"><span class="idiff right">}</span></span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="shell"><span class="o" style="font-weight: 600;"><span class="idiff left right">}</span></span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="shell"></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="shell"><span class="idiff left">test02</span><span class="o" style="font-weight: 600;"><span class="idiff right">(){</span></span></span>
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155
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo </span>ncov_minipipe <span class="nt" style="color: #000080;">--input</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">READS_TEST02</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-o</span> test02 <span class="nt" style="color: #000080;">--reference</span> <span class="nv" style="color: #008080;">$REF</span> <span class="se" style="color: #d14;">\</span></span>
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156
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="shell"> <span class="nt" style="color: #000080;">--conda_prefix</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TESTENVDIR</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">--blame</span></span>
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157
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="shell"> ncov_minipipe <span class="nt" style="color: #000080;">--input</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">READS_TEST02</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">--reason</span> <span class="nt" style="color: #000080;">-o</span> test02 <span class="nt" style="color: #000080;">--reference</span> <span class="nv" style="color: #008080;">$REF</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -160,8 +178,10 @@ run_tests(){</td>
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160
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="shell"> ncov_minipipe <span class="nt" style="color: #000080;">--reason</span> <span class="se" style="color: #d14;">\</span></span>
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161
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="shell"> <span class="nt" style="color: #000080;">--conf</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">echo </span>test02/<span class="k" style="font-weight: 600;">*</span>ncov_minipipe.config | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s1" style="color: #d14;">' '</span> <span class="nt" style="color: #000080;">-f1</span> <span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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162
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="shell"> <span class="nt" style="color: #000080;">--conda_prefix</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TESTENVDIR</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">--blame</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">snake_args</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">--debug</span> <span class="se" style="color: #d14;">\</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># test3</span></span>
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164
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="shell"></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="shell"></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="shell">test03<span class="o" style="font-weight: 600;">(){</span></span>
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165
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> test03/input</span>
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166
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> test03/input2</span>
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167
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-rf</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">READS_TEST02</span><span class="p">[0]</span><span class="k" style="font-weight: 600;">}</span> test03/input/200102_20-01222_nk0_S1_L001_R1_001.fastq.gz </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -175,9 +195,22 @@ run_tests(){</td>
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175
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="shell"></span>
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176
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="shell"> ncov_minipipe <span class="nt" style="color: #000080;">--input</span> test03/input <span class="nt" style="color: #000080;">--input</span> test03/input2 <span class="nt" style="color: #000080;">-o</span> test03/output <span class="nt" style="color: #000080;">--reference</span> <span class="nv" style="color: #008080;">$REF</span> <span class="se" style="color: #d14;">\</span></span>
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177
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="shell"> <span class="nt" style="color: #000080;">--conda_prefix</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TESTENVDIR</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">--reason</span> <span class="nt" style="color: #000080;">--run_id</span> <span class="s2" style="color: #d14;">"run01-202001"</span> <span class="se" style="color: #d14;">\</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="shell"> <span class="nt" style="color: #000080;">--blame</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">snake_args</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">--debug</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="shell"> <span class="nt" style="color: #000080;">--blame</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">snake_args</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">--debug</span> <span class="nt" style="color: #000080;">--cpus</span> 2</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="shell"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="shell">test04<span class="o" style="font-weight: 600;">(){</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> krakendb</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">pushd </span>krakendb</span>
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<td class="new_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> GRCh<span class="k" style="font-weight: 600;">*</span>/ <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>wget <span class="nt" style="color: #000080;">-nc</span> https://zenodo.org/record/4534746/files/GRCh38.p13_SC2_2021-02-08.tar.gz</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzvf</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz <span class="nt" style="color: #000080;">-C</span> ./</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="shell"></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">popd </span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span>ncov_minipipe <span class="nt" style="color: #000080;">--input</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">READS_TEST04</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">--reason</span> <span class="nt" style="color: #000080;">-o</span> test04 <span class="nt" style="color: #000080;">--reference</span> <span class="nv" style="color: #008080;">$REF</span> <span class="se" style="color: #d14;">\</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="shell"> <span class="nt" style="color: #000080;">--conda_prefix</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TESTENVDIR</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">--blame</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">snake_args</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">--debug</span> <span class="se" style="color: #d14;">\</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="shell"> <span class="nt" style="color: #000080;">--kraken</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">readlink</span> <span class="nt" style="color: #000080;">-f</span> krakendb/GRCh<span class="k" style="font-weight: 600;">*</span>/<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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179
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="shell"></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="shell"> deactivate_conda</span>
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181
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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182
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="shell"></span>
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183
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="shell"></span>
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