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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/bcbio">Debian Med / bcbio</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92">5c8848ab</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-02-10T16:24:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.6</pre>
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</ul>
<h4>28 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#d30b04166486087de34ff05cf278d3dd2ddd2360">
HISTORY.md
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<li class="file-stats">
<a href="#8875df48c18030126ef5ef5a6f5c93b23451fb9f">
MANIFEST.in
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#6cfbdb297f478b988ce7f28ee6c013bc814b7ed6">
bcbio/dragen/dragen.py
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<li class="file-stats">
<a href="#6b0954b64bb7025f3d13cbef18622daa684dbe1a">
bcbio/pipeline/main.py
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<li class="file-stats">
<a href="#28669a7ddccdf8ac47c577727840379bba16c871">
bcbio/pipeline/rnaseq.py
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<li class="file-stats">
<a href="#6a5842dd9e3c5daac8e6d62a34e4d60ab86b78bf">
bcbio/pipeline/run_info.py
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<li class="file-stats">
<a href="#4529c40caf2a26a49dd0e781055543aaecdd79fc">
bcbio/provenance/programs.py
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<li class="file-stats">
<a href="#b7e501c752cdb46dea3a09628c724f2111008fc6">
bcbio/variation/annotation.py
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<li class="file-stats">
<a href="#38e9a1f988377830cea6624ef40fa333dd9174f6">
bcbio/variation/vardict.py
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<li class="file-stats">
<a href="#c62737386ec58551581150d32baaafce9009f07f">
config/examples/rnaseq-seqc-getdata.sh
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<li class="file-stats">
<a href="#c13e78239a34bce87353625f73962da8afde8598">
config/examples/rnaseq-seqc.yaml
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<li class="file-stats">
<a href="#6519058175ec41a63e56cd70f874d5efabe85a5c">
config/examples/seqc.csv
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<li class="file-stats">
<a href="#6d2cadb523932676c6f1437d5a369d5b90c31af1">
config/genomes/GRCh37-resources.yaml
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<li class="file-stats">
<a href="#feed131f89893ff61e7bd1b941791558c255f866">
config/genomes/hg19-resources.yaml
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<li class="file-stats">
<a href="#234e8fcf6a3ef36167f45bd34532469e8aef57eb">
config/genomes/hg38-resources.yaml
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<li class="file-stats">
<a href="#959cc6564d1f47e19b8daea754836e8309db2e19">
<span class="new-file">
+
config/templates/purecn_ton.yaml
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<li class="file-stats">
<a href="#d4a01618e69ec23258bcf7f41f3a10f71f40ddee">
config/vcfanno/GRCh37-gemini.conf
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<li class="file-stats">
<a href="#062859ad0e9ca8b80ef940d89d80463771aa419e">
config/vcfanno/hg38-gemini.conf
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<li class="file-stats">
<a href="#90758652aa44d7aee266bd0d90a2fe01bf23ac55">
config/vcfanno/somatic.conf
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<li class="file-stats">
<a href="#06ab1978f5f7bbba6c3a94e3f4b306e4ddac4801">
docs/contents/bulk_rnaseq.md
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<li class="file-stats">
<a href="#b8ea2f27fdb24b27de13de2d32707e6af8788bda">
docs/contents/configuration.md
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<li class="file-stats">
<a href="#83f344ca0b114299c310d87b9ef098903138d93e">
docs/contents/installation.md
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<li class="file-stats">
<a href="#d780222435a775b157cca2d5946cddc237dd74d7">
docs/contents/purecn.md
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<li class="file-stats">
<a href="#b1655f936472b3a6a6a310218f78e1d19987454b">
requirements-conda.txt
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<li class="file-stats">
<a href="#19359a61ae2446b51b549167b014da2fcf265768">
requirements.txt
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<li class="file-stats">
<a href="#bacc76312ae1e30f71298a0e5abf86c8e5dbec70">
scripts/bcbio_setup_genome.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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</ul>
<h4>Changes:</h4>
<li id="d30b04166486087de34ff05cf278d3dd2ddd2360">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#d30b04166486087de34ff05cf278d3dd2ddd2360"><strong>HISTORY.md</strong></a>
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1
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.2.6 (in progress)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.2.7 (in progress)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.2.6 (04 February 2021)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">-</span> RNASeq: Fail more gracefully if SummarizedExperiment object cannot be created.</span>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">-</span> Fixes to handle DRAGEN BAM files from the first stage of UMI processing.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">-</span> Fix issue with double-annotating with dbSNP. Separating out somatic variant annotation into it's own vcfanno configuration.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.2.5 (01 January 2021)</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p">-</span> Joint calling for RNA-seq variant calling requires setting <span class="sb" style="color: #d14;">`jointcaller`</span> to bring it in line</span>
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<li id="8875df48c18030126ef5ef5a6f5c93b23451fb9f">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#8875df48c18030126ef5ef5a6f5c93b23451fb9f"><strong>MANIFEST.in</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,5 +9,7 @@ include tests/data/*.csv</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">include tests/data/automated/*.yaml</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">include tests/data/automated/*.ini</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">include tests/data/automated/tool-data/*.loc</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">include tests/data/variants/*.vcf</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">include tests/data/variants/*.tbi</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">include bcbio/scripts/R/*.R</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">include bcbio/scripts/R/*.Rmd</span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -8,11 +8,11 @@ Validated, scalable, community developed variant calling, RNA-seq and small RNA</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Features</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="p">*</span> Community developed: We welcome contributors with the goal of overcoming the biological, algorithmic and computational challenges that face individual developers working on complex pipelines in quickly changing research areas. See our <span class="p">[</span><span class="nv" style="color: #008080;">users page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bcbio-nextgen.readthedocs.io/en/latest/contents/<span class="idiff left right">about.html#users</span></span><span class="p">)</span> for examples of bcbio-nextgen deployments, and the <span class="p">[</span><span class="nv" style="color: #008080;">developer documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bcbio-nextgen.readthedocs.io/en/latest/contents/development.html</span><span class="p">)</span> for tips on contributing.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">*</span> Community developed: We welcome contributors with the goal of overcoming the biological, algorithmic and computational challenges that face individual developers working on complex pipelines in quickly changing research areas. See our <span class="p">[</span><span class="nv" style="color: #008080;">users page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bcbio-nextgen.readthedocs.io/en/latest/contents/<span class="idiff left right">users.html</span></span><span class="p">)</span> for examples of bcbio-nextgen deployments, and the <span class="p">[</span><span class="nv" style="color: #008080;">developer documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bcbio-nextgen.readthedocs.io/en/latest/contents/development.html</span><span class="p">)</span> for tips on contributing.</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="p">*</span> Installation: <span class="p">[</span><span class="nv" style="color: #008080;">A single installer script</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bcbio-nextgen.readthedocs.io/en/latest/contents/installation.html#automated</span><span class="p">)</span> prepares all third party software, data libraries and system configuration files.</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Automated validation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bcb.io/2014/05/12/wgs-trio-variant-evaluation/</span><span class="p">)</span>: Compare variant calls against common reference materials or sample specific SNP arrays to ensure call correctness. Incorporation of multiple approaches for alignment, preparation and variant calling enable unbiased comparisons of algorithms.</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="p">*</span> Distributed: Focus on <span class="p">[</span><span class="nv" style="color: #008080;">parallel analysis and scaling</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bcb.io/2013/05/22/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis/</span><span class="p">)</span> to handle large population studies and whole genome analysis. Runs on single multicore computers, in compute clusters using <span class="p">[</span><span class="nv" style="color: #008080;">IPython parallel</span><span class="p">](</span><span class="sx" style="color: #d14;">https://ipyparallel.readthedocs.io/en/latest/</span><span class="p">)</span>, or on the Amazon cloud. See the <span class="p">[</span><span class="nv" style="color: #008080;">parallel documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bcbio-nextgen.readthedocs.org/en/latest/contents/parallel.html</span><span class="p">)</span> for full details.</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="p">*</span> Multiple analysis algorithms: bcbio-nextgen provides configurable <span class="p">[</span><span class="nv" style="color: #008080;">variant calling<span class="idiff left">, RNA-seq and small RNA pipelines</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">https://bcbio-nextgen.readthedocs.io/en/latest/contents/pipelines.html</span></span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">*</span> Multiple analysis algorithms: bcbio-nextgen provides configurable <span class="p">[</span><span class="nv" style="color: #008080;">variant calling<span class="idiff left"> (small and copy number), RNA-seq, ATAC-seq, , BS-Seq, SC RNA-seq, and small RNA pipelines</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">https://bcbio-nextgen.readthedocs.io/en/latest/</span></span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Quick start</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></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">@@ -20,7 +20,7 @@ Validated, scalable, community developed variant calling, RNA-seq and small RNA</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"> <span class="p">```</span><span class="nl">shell script</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="sb" style="color: #d14;"> wget https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="sb" style="color: #d14;"> python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local \</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --genomes <span class="idiff left right">GRCh37</span> --aligners bwa --aligners bowtie2</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --genomes <span class="idiff left right">hg38</span> --aligners bwa --aligners bowtie2</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"> <span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"> producing an editable <span class="p">[</span><span class="nv" style="color: #008080;">system configuration file</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/bcbio/bcbio-nextgen/blob/master/config/bcbio_system.yaml</span><span class="p">)</span> referencing the installed software, data and system information.</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<li id="6cfbdb297f478b988ce7f28ee6c013bc814b7ed6">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#6cfbdb297f478b988ce7f28ee6c013bc814b7ed6"><strong>bcbio/dragen/dragen.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">@@ -6,9 +6,10 @@ from bcbio.pipeline import config_utils</td>
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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;">bcbio.provenance</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">do</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.distributed.transaction</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">file_transaction</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">file_exists</span><span class="p">,</span> <span class="n" style="color: #333;">splitext_plus</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">bam</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">bam</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">broad</span></span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.log</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">logger</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fix_umi_dragen_bam</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">bam</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="LC14" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;"> fixes the UMI BAM from DRAGEN. Accepts a pre UMI collapsed BAM file and</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,12 +38,18 @@ def add_fgbio_tags(in_bam, out_bam, data):</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">samtools</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="p">.</span><span class="n" style="color: #333;">get_program</span><span class="p">(</span><span class="s" style="color: #d14;">"samtools"</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="LC40" class="line" lang="python"> <span class="n" style="color: #333;">bamsormadup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="p">.</span><span class="n" style="color: #333;">get_program</span><span class="p">(</span><span class="s" style="color: #d14;">"bamsormadup"</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="LC41" class="line" lang="python"> <span class="n" style="color: #333;">fgbio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="p">.</span><span class="n" style="color: #333;">get_program</span><span class="p">(</span><span class="s" style="color: #d14;">"fgbio"</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="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;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">out_bam</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_bam</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;">tmpdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">tx_out_bam</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;">jvm_opts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_fgbio_jvm_opts</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</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="LC46" class="line" lang="python"> <span class="n" style="color: #333;">tx_out_dup</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%s-markdup"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">splitext_plus</span><span class="p">(</span><span class="n" style="color: #333;">tx_out_bam</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="LC47" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">samtools</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> view -b </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">in_bam</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> | "</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">bamsormadup</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> outputformat=sam tmpfile=</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">tx_out_dup</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> | "</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"awk '/^@/ {{print;next}} {{N=split($1,n,</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">:</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">);print $0 </span><span class="se" style="color: #d14;">\"\t</span><span class="s" style="color: #d14;">RX:Z:</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> n[N]}}' | "</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fgbio</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">jvm_opts</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> SortBam -i /dev/stdin -o /dev/stdout -s Queryname |"</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fgbio</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">jvm_opts</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> SetMateInformation | "</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fgbio</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">jvm_opts</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> SortBam -i /dev/stdin -o /dev/stdout -s Coordinate |"</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">samtools</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> view -bh > </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">tx_out_bam</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"Adding MC/MQ/RX tags to DRAGEN BAM file </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">in_bam</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">."</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">message</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">@@ -54,3 +61,26 @@ def has_fgbio_tags(in_bam):</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">FGBIO_TAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="s" style="color: #d14;">"MC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"MQ"</span><span class="p">,</span> <span class="s" style="color: #d14;">"RX"</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bam</span><span class="p">.</span><span class="n" style="color: #333;">has_tags</span><span class="p">(</span><span class="n" style="color: #333;">in_bam</span><span class="p">,</span> <span class="n" style="color: #333;">FGBIO_TAGS</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_fgbio_jvm_opts</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">scale_factor</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="LC66" class="line" lang="python"> <span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">mem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_cores_memory</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="LC67" class="line" lang="python"> <span class="n" style="color: #333;">resources</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="p">.</span><span class="n" style="color: #333;">get_resources</span><span class="p">(</span><span class="s" style="color: #d14;">"fgbio"</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"config"</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;">jvm_opts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">resources</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"jvm_opts"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"-Xms750m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-Xmx4g"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">scale_factor</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">scale_factor</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">jvm_opts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="p">.</span><span class="n" style="color: #333;">adjust_opts</span><span class="p">(</span><span class="n" style="color: #333;">jvm_opts</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"algorithm"</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">"memory_adjust"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="p">{</span><span class="s" style="color: #d14;">"direction"</span><span class="p">:</span> <span class="s" style="color: #d14;">"increase"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="s" style="color: #d14;">"magnitude"</span><span class="p">:</span> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">//</span> <span class="n" style="color: #333;">scale_factor</span><span class="p">}}})</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">jvm_opts</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">broad</span><span class="p">.</span><span class="n" style="color: #333;">get_default_jvm_opts</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;">jvm_opts</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;">jvm_opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">jvm_opts</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" --tmp-dir %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tmpdir</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_cores_memory</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">downscale</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="s" style="color: #d14;">"""Retrieve cores and memory, using samtools as baseline.</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;"> For memory, scaling down because we share with alignment and de-duplication.</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">resources</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="p">.</span><span class="n" style="color: #333;">get_resources</span><span class="p">(</span><span class="s" style="color: #d14;">"samtools"</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"config"</span><span class="p">])</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">num_cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"config"</span><span class="p">][</span><span class="s" style="color: #d14;">"algorithm"</span><span class="p">].</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"num_cores"</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;">max_mem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="p">.</span><span class="n" style="color: #333;">adjust_memory</span><span class="p">(</span><span class="n" style="color: #333;">resources</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"memory"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2G"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">downscale</span><span class="p">,</span> <span class="s" style="color: #d14;">"decrease"</span><span class="p">).</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">num_cores</span><span class="p">,</span> <span class="n" style="color: #333;">max_mem</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#6b0954b64bb7025f3d13cbef18622daa684dbe1a"><strong>bcbio/pipeline/main.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">@@ -272,6 +272,8 @@ def rnaseqpipeline(config, run_info_yaml, parallel, dirs, samples):</td>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">dirs</span><span class="p">,</span> <span class="s" style="color: #d14;">"qc"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">run_parallel</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">profile</span><span class="p">.</span><span class="n" style="color: #333;">report</span><span class="p">(</span><span class="s" style="color: #d14;">"quality control"</span><span class="p">,</span> <span class="n" style="color: #333;">dirs</span><span class="p">):</span></span>
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qcsummary</span><span class="p">.</span><span class="n" style="color: #333;">generate_parallel</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">run_parallel</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;">with</span> <span class="n" style="color: #333;">profile</span><span class="p">.</span><span class="n" style="color: #333;">report</span><span class="p">(</span><span class="s" style="color: #d14;">"create SummarizedExperiment object"</span><span class="p">,</span> <span class="n" style="color: #333;">dirs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rnaseq</span><span class="p">.</span><span class="n" style="color: #333;">load_summarizedexperiment</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">profile</span><span class="p">.</span><span class="n" style="color: #333;">report</span><span class="p">(</span><span class="s" style="color: #d14;">"upload"</span><span class="p">,</span> <span class="n" style="color: #333;">dirs</span><span class="p">):</span></span>
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276
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_parallel</span><span class="p">(</span><span class="s" style="color: #d14;">"upload_samples"</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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277
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sample</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#28669a7ddccdf8ac47c577727840379bba16c871"><strong>bcbio/pipeline/rnaseq.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">@@ -482,17 +482,6 @@ def combine_files(samples):</td>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;">dexseq_combined</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="LC483" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spikein</span><span class="p">.</span><span class="n" style="color: #333;">combine_spikein</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"> <span class="n" style="color: #333;">tximport</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_tximport</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="LC485" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># don't fail runs while we get dependencies straightened out</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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487
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># we need metadata.csv to generate SE</span></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="python"> <span class="n" style="color: #333;">work_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="p">.</span><span class="n" style="color: #333;">get_work_dir</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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489
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="python"> <span class="n" style="color: #333;">metadata_file</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;">work_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"metadata.csv"</span><span class="p">)</span></span>
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490
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<pre style="margin: 0;">-<span id="LC490" 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;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">metadata_file</span><span class="p">):</span></span>
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491
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">qcsummary</span><span class="p">.</span><span class="n" style="color: #333;">_merge_metadata</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="python"> <span class="n" style="color: #333;">summarized_experiment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_summarizedexperiment</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="LC493" class="line" lang="python"> <span class="n" style="color: #333;">qc_report</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">generate_se_qc_report</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="LC494" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">summarized_experiment</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="LC485" class="line" lang="python"> <span class="n" style="color: #333;">updated_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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497
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">data</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dd</span><span class="p">.</span><span class="n" style="color: #333;">sample_data_iterator</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">):</span></span>
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498
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">combined</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -513,7 +502,6 @@ def combine_files(samples):</td>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gtf_file</span><span class="p">:</span></span>
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="p">.</span><span class="n" style="color: #333;">set_tx2gene</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">tx2gene_file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC504" 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;">dd</span><span class="p">.</span><span class="n" style="color: #333;">set_tximport</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">tximport</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="p">.</span><span class="n" style="color: #333;">set_summarized_experiment</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">summarized_experiment</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="python"> <span class="n" style="color: #333;">updated_samples</span><span class="p">.</span><span class="n" style="color: #333;">append</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="LC506" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">updated_samples</span></span>
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<pre style="margin: 0;"> <span id="LC507" 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">@@ -564,30 +552,44 @@ def load_tximport(data):</td>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">{</span><span class="s" style="color: #d14;">"gene_tpm"</span><span class="p">:</span> <span class="n" style="color: #333;">tpm_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python"> <span class="s" style="color: #d14;">"gene_counts"</span><span class="p">:</span> <span class="n" style="color: #333;">counts_file</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">load_summarizedexperiment</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">data</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">load_summarizedexperiment</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">samples</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python"> <span class="s" style="color: #d14;">""" create summarizedexperiment rds object</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python"><span class="s" style="color: #d14;"> fails with n_samples = 1 """</span></span>
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570
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># using r36 (4.0) - will eventually drop R3.5</span></span>
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571
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="python"> <span class="n" style="color: #333;">rcmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Rscript_cmd</span><span class="p">(</span><span class="s" style="color: #d14;">"r36"</span><span class="p">)</span></span>
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572
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="python"> <span class="n" style="color: #333;">se_script</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;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">),</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">pardir</span><span class="p">,</span> <span class="s" style="color: #d14;">"scripts"</span><span class="p">,</span></span>
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573
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python"> <span class="s" style="color: #d14;">"R"</span><span class="p">,</span> <span class="s" style="color: #d14;">"bcbio2se.R"</span><span class="p">)</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samples</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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574
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="python"> <span class="n" style="color: #333;">work_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="p">.</span><span class="n" style="color: #333;">get_work_dir</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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575
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="python"> <span class="n" style="color: #333;">out_dir</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;">work_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"salmon"</span><span class="p">)</span></span>
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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="python"> <span class="n" style="color: #333;">out_file</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;">out_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"bcbio-se.rds"</span><span class="p">)</span></span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">):</span></span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out_file</span></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">:</span></span>
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580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">rcmd</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> --vanilla </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">se_script</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">work_dir</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">tx_out_file</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span>
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581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"Loading SummarizedExperiment."</span></span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">message</span><span class="p">)</span></span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out_file</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="python"> <span class="n" style="color: #333;">summarized_experiment</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;">out_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"bcbio-se.rds"</span><span class="p">)</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">summarized_experiment</span><span class="p">):</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">summarized_experiment</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_file</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;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">rcmd</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> --vanilla </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">se_script</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">work_dir</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">tx_out_file</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"Loading SummarizedExperiment."</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</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;">do</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">message</span><span class="p">)</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
573
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<pre style="margin: 0;">+<span id="LC573" 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;">"SE creation failed"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">summarized_experiment</span><span class="p">):</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="python"> <span class="n" style="color: #333;">se_qc_report</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">generate_se_qc_report</span><span class="p">(</span><span class="n" style="color: #333;">work_dir</span><span class="p">)</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="python"> <span class="n" style="color: #333;">se_qc_report</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" 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;">"SE QC failed"</span><span class="p">)</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="python"> <span class="n" style="color: #333;">updated_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">data</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dd</span><span class="p">.</span><span class="n" style="color: #333;">sample_data_iterator</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">):</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" 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;">dd</span><span class="p">.</span><span class="n" style="color: #333;">set_summarized_experiment</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">summarized_experiment</span><span class="p">)</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="python"> <span class="n" style="color: #333;">updated_samples</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">data</span><span class="p">])</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">updated_samples</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">samples</span></span>
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584
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587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="python"></span>
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585
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_se_qc_report</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">data</span></span><span class="p">):</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_se_qc_report</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">work_dir</span></span><span class="p">):</span></span>
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="python"> <span class="s" style="color: #d14;">""" generate QC report based on SE RDS object"""</span></span>
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590
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="python"> <span class="n" style="color: #333;">rcmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Rscript_cmd</span><span class="p">(</span><span class="s" style="color: #d14;">"r36"</span><span class="p">)</span></span>
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="python"> <span class="n" style="color: #333;">qc_script</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;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">),</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">pardir</span><span class="p">,</span> <span class="s" style="color: #d14;">"scripts"</span><span class="p">,</span></span>
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592
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="python"> <span class="s" style="color: #d14;">"R"</span><span class="p">,</span> <span class="s" style="color: #d14;">"se2qc.Rmd"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="python"> <span class="n" style="color: #333;">work_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="p">.</span><span class="n" style="color: #333;">get_work_dir</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="python"> <span class="n" style="color: #333;">out_file</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;">work_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"qc"</span><span class="p">,</span> <span class="s" style="color: #d14;">"bcbio-se.html"</span><span class="p">)</span></span>
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594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="python"> <span class="n" style="color: #333;">rds_file</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;">work_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"salmon"</span><span class="p">,</span> <span class="s" style="color: #d14;">"bcbio-se.rds"</span><span class="p">)</span></span>
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595
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#6a5842dd9e3c5daac8e6d62a34e4d60ab86b78bf"><strong>bcbio/pipeline/run_info.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">@@ -726,12 +726,15 @@ def _check_hetcaller(item):</td>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python"> <span class="s" style="color: #d14;">"""Ensure upstream SV callers requires to heterogeneity analysis are available.</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="python"><span class="s" style="color: #d14;"> purecn has its own segmentation - no need in cnvkit or gatk-cnv</span></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="python"> <span class="n" style="color: #333;">svs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_as_list</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">,</span> <span class="s" style="color: #d14;">"svcaller"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="python"> <span class="n" style="color: #333;">hets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_as_list</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">,</span> <span class="s" style="color: #d14;">"hetcaller"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hets</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">([</span><span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">svs</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="p">[</span><span class="s" style="color: #d14;">"titancna"</span><span class="p">]]):</span></span>
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">([</span><span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">svs</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="p">[</span><span class="s" style="color: #d14;">"cnvkit"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gatk-cnv"</span><span class="p">]]):</span></span>
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<pre style="margin: 0;">-<span id="LC733" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Heterogeneity caller used but need CNV calls. Add `gatk-cnv` "</span></span>
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="python"> <span class="s" style="color: #d14;">"or `cnvkit` to `svcaller` in sample: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">item</span><span class="p">[</span><span class="s" style="color: #d14;">"description"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="python"> <span class="n" style="color: #333;">svs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_as_list</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">,</span> <span class="s" style="color: #d14;">"svcaller"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="python"> <span class="n" style="color: #333;">needing_cnv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hets</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">svs</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"titancna"</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="python"> <span class="n" style="color: #333;">needing_cnv</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">needing_cnv</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">([</span><span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">svs</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="p">[</span><span class="s" style="color: #d14;">"cnvkit"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gatk-cnv"</span><span class="p">]]):</span></span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Heterogeneity caller(s) %s used but need CNV calls. Add `gatk-cnv` "</span></span>
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="python"> <span class="s" style="color: #d14;">"or `cnvkit` to `svcaller` in sample: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</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;">needing_cnv</span><span class="p">),</span> <span class="n" style="color: #333;">item</span><span class="p">[</span><span class="s" style="color: #d14;">"description"</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_jointcaller</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="LC740" class="line" lang="python"> <span class="s" style="color: #d14;">"""Ensure specified jointcaller is valid.</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#4529c40caf2a26a49dd0e781055543aaecdd79fc"><strong>bcbio/provenance/programs.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">@@ -35,13 +35,13 @@ _cl_progs = [{"cmd": "bamtofastq", "name": "biobambam",</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="p">{</span><span class="s" style="color: #d14;">"cmd"</span><span class="p">:</span> <span class="s" style="color: #d14;">"vcflib"</span><span class="p">,</span> <span class="s" style="color: #d14;">"has_cl_version"</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="LC36" class="line" lang="python"> <span class="p">{</span><span class="s" style="color: #d14;">"cmd"</span><span class="p">:</span> <span class="s" style="color: #d14;">"featureCounts"</span><span class="p">,</span> <span class="s" style="color: #d14;">"args"</span><span class="p">:</span> <span class="s" style="color: #d14;">"-v"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stdout_flag"</span><span class="p">:</span> <span class="s" style="color: #d14;">"featureCounts"</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;">_manifest_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">'bcbio-variation'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bioconductor-bubbletree'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cufflinks'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left">atropos'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'</span>bcbio-variation'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bioconductor-bubbletree'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cufflinks'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">'cnvkit'</span><span class="p">,</span> <span class="s" style="color: #d14;">'fgbio'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gatk4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'hisat2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sailfish'</span><span class="p">,</span> <span class="s" style="color: #d14;">'salmon'</span><span class="p">,</span> <span class="s" style="color: #d14;">'grabix'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">'htseq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'lumpy-sv'</span><span class="p">,</span> <span class="s" style="color: #d14;">'manta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'break-point-inspector'</span><span class="p">,</span> <span class="s" style="color: #d14;">'metasv'</span><span class="p">,</span> <span class="s" style="color: #d14;">'multiqc'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">'seq2c'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mirdeep2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'oncofuse'</span><span class="p">,</span> <span class="s" style="color: #d14;">'picard'</span><span class="p">,</span> <span class="s" style="color: #d14;">'phylowgs'</span><span class="p">,</span> <span class="s" style="color: #d14;">'platypus-variant'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'rapmap'</span><span class="p">,</span> <span class="s" style="color: #d14;">'star'</span><span class="p">,</span> <span class="s" style="color: #d14;">'rtg-tools'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sambamba'</span><span class="p">,</span> <span class="s" style="color: #d14;">'samblaster'</span><span class="p">,</span> <span class="s" style="color: #d14;">'scalpel'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">'seqbuster'</span><span class="p">,</span> <span class="s" style="color: #d14;">'snpeff'</span><span class="p">,</span> <span class="s" style="color: #d14;">'vardict'</span><span class="p">,</span> <span class="s" style="color: #d14;">'vardict-java'</span><span class="p">,</span> <span class="s" style="color: #d14;">'varscan'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left">ensembl-vep'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'</span>vt'</span><span class="p">,</span> <span class="s" style="color: #d14;">'wham'</span><span class="p">,</span> <span class="s" style="color: #d14;">'umis'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">'seqbuster'</span><span class="p">,</span> <span class="s" style="color: #d14;">'snpeff'</span><span class="p">,</span> <span class="s" style="color: #d14;">'vardict'</span><span class="p">,</span> <span class="s" style="color: #d14;">'vardict-java'</span><span class="p">,</span> <span class="s" style="color: #d14;">'varscan'</span><span class="p">,</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'ensembl-vep'</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">'vt'</span><span class="p">,</span> <span class="s" style="color: #d14;">'wham'</span><span class="p">,</span> <span class="s" style="color: #d14;">'umis'</span><span class="p">]</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;">_broad_versioner</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC47" 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="n" style="color: #333;">config</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#b7e501c752cdb46dea3a09628c724f2111008fc6"><strong>bcbio/variation/annotation.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">@@ -46,7 +46,7 @@ def get_gatk_annotations(config, include_depth=True, include_baseqranksum=True,</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">anns</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">finalize_vcf</span><span class="p">(</span><span class="n" style="color: #333;">in_file</span><span class="p">,</span> <span class="n" style="color: #333;">variantcaller</span><span class="p">,</span> <span class="n" style="color: #333;">items</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"""Perform cleanup <span class="idiff left right">and dbSNP annotation </span>of the final VCF.</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"""Perform cleanup of the final VCF.</span></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="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> - Adds contigs to header for bcftools compatibility</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"> - adds sample information for tumor/normal</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">@@ -60,9 +60,6 @@ def finalize_vcf(in_file, variantcaller, items):</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">post_cl</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;">cls</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" | "</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">post_cl</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="LC63" class="line" lang="python"> <span class="n" style="color: #333;">dbsnp_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tz</span><span class="p">.</span><span class="n" style="color: #333;">get_in</span><span class="p">((</span><span class="s" style="color: #d14;">"genome_resources"</span><span class="p">,</span> <span class="s" style="color: #d14;">"variation"</span><span class="p">,</span> <span class="s" style="color: #d14;">"dbsnp"</span><span class="p">),</span> <span class="n" style="color: #333;">items</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="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dbsnp_file</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_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_add_dbsnp</span><span class="p">(</span><span class="n" style="color: #333;">in_file</span><span class="p">,</span> <span class="n" style="color: #333;">dbsnp_file</span><span class="p">,</span> <span class="n" style="color: #333;">items</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="n" style="color: #333;">post_cl</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vcfutils</span><span class="p">.</span><span class="n" style="color: #333;">bgzip_and_index</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="n" style="color: #333;">items</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="s" style="color: #d14;">"config"</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -133,45 +130,6 @@ def _update_header(orig_vcf, base_file, new_lines, chrom_process_fn=None):</td>
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">out_handle</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">chrom_line</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new_header</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"><span class="n" style="color: #333;">_DBSNP_TEMPLATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"><span class="s" style="color: #d14;">[[annotation]]</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"><span class="s" style="color: #d14;">file="%s"</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"><span class="s" style="color: #d14;">fields=["ID"]</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"><span class="s" style="color: #d14;">names=["rs_ids"]</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"><span class="s" style="color: #d14;">ops=["concat"]</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"><span class="s" style="color: #d14;">[[postannotation]]</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"><span class="s" style="color: #d14;">name="ID"</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"><span class="s" style="color: #d14;">fields=["rs_ids"]</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"><span class="s" style="color: #d14;">op="setid"</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"><span class="s" style="color: #d14;">type="String"</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;">[[postannotation]]</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"><span class="s" style="color: #d14;">fields=["rs_ids"]</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"><span class="s" style="color: #d14;">op="delete"</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_add_dbsnp</span><span class="p">(</span><span class="n" style="color: #333;">orig_file</span><span class="p">,</span> <span class="n" style="color: #333;">dbsnp_file</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</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;">post_cl</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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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="s" style="color: #d14;">"""Annotate a VCF file with dbSNP.</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"><span class="s" style="color: #d14;"> vcfanno has flexible matching for NON_REF gVCF positions, matching</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"><span class="s" style="color: #d14;"> at position and REF allele, matching ALT NON_REF as a wildcard.</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">orig_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcfutils</span><span class="p">.</span><span class="n" style="color: #333;">bgzip_and_index</span><span class="p">(</span><span class="n" style="color: #333;">orig_file</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"config"</span><span class="p">])</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">out_file</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%s-wdbsnp.vcf.gz"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">splitext_plus</span><span class="p">(</span><span class="n" style="color: #333;">orig_file</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" 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;">utils</span><span class="p">.</span><span class="n" style="color: #333;">file_uptodate</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="n" style="color: #333;">orig_file</span><span class="p">):</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">:</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">conf_file</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;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">),</span> <span class="s" style="color: #d14;">"dbsnp.conf"</span><span class="p">)</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" 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;">conf_file</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;">out_handle</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">out_handle</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">_DBSNP_TEMPLATE</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;">normpath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dd</span><span class="p">.</span><span class="n" style="color: #333;">get_work_dir</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">dbsnp_file</span><span class="p">)))</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" 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;">post_cl</span><span class="p">:</span> <span class="n" style="color: #333;">post_cl</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="p">.</span><span class="n" style="color: #333;">get_num_cores</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="LC170" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"vcfanno -p {cores} {conf_file} {orig_file} | {post_cl} "</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="s" style="color: #d14;">"bgzip -c > {tx_out_file}"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="nb" style="color: #0086b3;">locals</span><span class="p">()),</span> <span class="s" style="color: #d14;">"Annotate with dbSNP"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vcfutils</span><span class="p">.</span><span class="n" style="color: #333;">bgzip_and_index</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"config"</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_context_files</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="LC134" class="line" lang="python"> <span class="s" style="color: #d14;">"""Retrieve pre-installed annotation files for annotating genome context.</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#38e9a1f988377830cea6624ef40fa333dd9174f6"><strong>bcbio/variation/vardict.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">@@ -46,9 +46,10 @@ def _vardict_options_from_config(items, config, out_file, target=None, is_rnaseq</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># SV calling will be worked on as a separate step</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">vardict_cl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_vardict_command</span><span class="p">(</span><span class="n" style="color: #333;">items</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="LC48" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">programs</span><span class="p">.</span><span class="n" style="color: #333;">get_version_manifest</span><span class="p">(</span><span class="n" style="color: #333;">vardict_cl</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># turn off structural variants</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vardict_cl</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">version</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="p">((</span><span class="n" style="color: #333;">vardict_cl</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"vardict-java"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">LooseVersion</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">LooseVersion</span><span class="p">(</span><span class="s" style="color: #d14;">"1.5.5"</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">or</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">vardict_cl</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"vardict"</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">LooseVersion</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">version</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">LooseVersion</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"2018.07.25"</span></span><span class="p"><span class="idiff right">)</span>))):</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">vardict_cl</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"vardict"</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;">opts</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="s" style="color: #d14;">"--nosv"</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vardict_cl</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">version</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">vardict_cl</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"vardict-java"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">LooseVersion</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">LooseVersion</span><span class="p">(</span><span class="s" style="color: #d14;">"1.5.6"</span><span class="p">))):</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#c62737386ec58551581150d32baaafce9009f07f"><strong>config/examples/rnaseq-seqc-getdata.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">@@ -2,20 +2,22 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-eu</span> <span class="nt" style="color: #000080;">-o</span> pipefail</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># We need about 100Gb for the input files. Confirm we have the space.</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">REQ_DISK_SPACE</span><span class="o" style="font-weight: 600;">=</span>100</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">REQ_DISK_SPACE</span><span class="o" style="font-weight: 600;">=</span>100<span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">df</span> <span class="nt" style="color: #000080;">--block-size</span><span class="o" style="font-weight: 600;">=</span>G <span class="nt" style="color: #000080;">--output</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'avail'</span> <span class="nb" style="color: #0086b3;">.</span> | <span class="nb" style="color: #0086b3;">sed </span>s/G//g | <span class="nb" style="color: #0086b3;">awk</span> <span class="nt" style="color: #000080;">-v</span> <span class="nv" style="color: #008080;">req_disk_space</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">REQ_DISK_SPACE</span><span class="k" style="font-weight: 600;">}</span> <span class="s1" style="color: #d14;">'{ if ($1 !~ /Avail/ && $1 < req_disk_space ) printf("Warning: Not enough disk space.\n Warning: Requires %sGb in total but only has %sGb.\n", req_disk_space, $1) }'</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> input</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> seqc/input</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell">wget <span class="nt" style="color: #000080;">--no-check-certificate</span> https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/examples/rnaseq-seqc.yaml</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>input</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span><span class="idiff left right">seqc/</span>input</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>SAMPLE <span class="k" style="font-weight: 600;">in </span>SRR950078 SRR950079 SRR950080 SRR950081 SRR950082 SRR950083</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>wget <span class="nt" style="color: #000080;">-O</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>_1.fastq.gz</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"> wget <span class="nt" style="color: #000080;">-O</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>_2.fastq.gz</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">do </span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>wget <span class="nt" style="color: #000080;">-c</span> <span class="nt" style="color: #000080;">-O</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>_1.fastq.gz</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"> wget <span class="nt" style="color: #000080;">-c</span> <span class="nt" style="color: #000080;">-O</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>_2.fastq.gz</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">done </span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ../../</span>
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17
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell">wget <span class="nt" style="color: #000080;">--no-check-certificate</span> https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/examples/seqc.csv</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">wget <span class="nt" style="color: #000080;">-<span class="idiff left">c</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff right">-</span>-no-check-certificate</span> https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/examples/seqc.csv</span>
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19
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ../</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell">bcbio_nextgen.py <span class="nt" style="color: #000080;">-w</span> template rnaseq-seqc.yaml input/seqc.csv input</span></pre>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">bcbio_nextgen.py <span class="nt" style="color: #000080;">-w</span> template rnaseq-seqc.yaml seqc.csv seqc/input/<span class="k" style="font-weight: 600;">*</span>.gz</span></pre>
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<li id="c13e78239a34bce87353625f73962da8afde8598">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#c13e78239a34bce87353625f73962da8afde8598"><strong>config/examples/rnaseq-seqc.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">@@ -4,8 +4,12 @@ details:</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">analysis</span><span class="pi">:</span> <span class="s" style="color: #d14;">RNA-seq</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">genome_build</span><span class="pi">:</span> <span class="s" style="color: #d14;">hg38</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">algorithm</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;">quality_format</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">S</span>tandard</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">quality_format</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">s</span>tandard</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">aligner</span><span class="pi">:</span> <span class="s" style="color: #d14;">star</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">strandedness</span><span class="pi">:</span> <span class="s" style="color: #d14;">unstranded</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"><span class="na" style="color: #008080;">upload</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">dir</span><span class="pi">:</span> <span class="s" style="color: #d14;">../final</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">resources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">star</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">cores</span><span class="pi">:</span> <span class="m" style="color: #099;">10</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">memory</span><span class="pi">:</span> <span class="s" style="color: #d14;">10G</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#6519058175ec41a63e56cd70f874d5efabe85a5c"><strong>config/examples/seqc.csv</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">samplename,description,<span class="idiff left right">panel</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">samplename,description,<span class="idiff left right">category</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">SRR950078,UHRR_rep1,UHRR</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">SRR950079,HBRR_rep1,HBRR</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">SRR950080,UHRR_rep2,UHRR</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">SRR950081,HBRR_rep2,HBRR</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">SRR950082,UHRR_rep3,UHRR</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">SRR950083,HBRR_rep3,HBRR</span></pre>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">SRR950084,UHRR_rep4,UHRR</span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#6d2cadb523932676c6f1437d5a369d5b90c31af1"><strong>config/genomes/GRCh37-resources.yaml</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="m" style="color: #099;">5<span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="m" style="color: #099;">5<span class="idiff left right">5</span></span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">aliases</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">human</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,7 +6,7 @@ aliases:</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">ensembl</span><span class="pi">:</span> <span class="s" style="color: #d14;">homo_sapiens_merged_vep_100_GRCh37</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">variation</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">dbsnp</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/dbsnp<span class="idiff left right">-151</span>.vcf.gz</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">dbsnp</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/dbsnp.vcf.gz</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">train_hapmap</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/hapmap_3.3.vcf.gz</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">train_omni</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/1000G_omni2.5.vcf.gz</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">train_1000g</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/1000G_phase1.snps.high_confidence.vcf.gz</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#feed131f89893ff61e7bd1b941791558c255f866"><strong>config/genomes/hg19-resources.yaml</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="m" style="color: #099;">5<span class="idiff left right">6</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="m" style="color: #099;">5<span class="idiff left right">7</span></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">aliases</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">human</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</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">@@ -6,7 +6,7 @@ aliases:</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">ensembl</span><span class="pi">:</span> <span class="s" style="color: #d14;">homo_sapiens_merged_vep_100_GRCh37</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">variation</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">dbsnp</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/dbsnp<span class="idiff left right">-151</span>.vcf.gz</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">dbsnp</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/dbsnp.vcf.gz</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">train_hapmap</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/hapmap_3.3.vcf.gz</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">train_omni</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/1000G_omni2.5.vcf.gz</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">train_1000g</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/1000G_phase1.snps.high_confidence.vcf.gz</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#234e8fcf6a3ef36167f45bd34532469e8aef57eb"><strong>config/genomes/hg38-resources.yaml</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="m" style="color: #099;">4<span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="m" style="color: #099;">4<span class="idiff left right">5</span></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">aliases</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">human</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,7 +6,7 @@ aliases:</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">ensembl</span><span class="pi">:</span> <span class="s" style="color: #d14;">homo_sapiens_merged_vep_100_GRCh38</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">variation</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">dbsnp</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/dbsnp<span class="idiff left right">-153</span>.vcf.gz</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">dbsnp</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/dbsnp.vcf.gz</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">dbnsfp</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/dbNSFP.txt.gz</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">dbscsnv</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/dbscSNV.txt.gz</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">train_hapmap</span><span class="pi">:</span> <span class="s" style="color: #d14;">../variation/hapmap_3.3.vcf.gz</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#959cc6564d1f47e19b8daea754836e8309db2e19"><strong>config/templates/purecn_ton.yaml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Tumor only PureCN analysis with a PON (panel of normals)</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">details</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">analysis</span><span class="pi">:</span> <span class="s" style="color: #d14;">variant2</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">genome_build</span><span class="pi">:</span> <span class="s" style="color: #d14;">hg38</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">algorithm</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">aligner</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">svcaller</span><span class="pi">:</span> <span class="s" style="color: #d14;">purecn</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">variant_regions</span><span class="pi">:</span> <span class="s" style="color: #d14;">/path/ton/config/panel.bed</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">variantcaller</span><span class="pi">:</span> <span class="s" style="color: #d14;">mutect2</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">background</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">variant</span><span class="pi">:</span> <span class="s" style="color: #d14;">/path/ton/config/pon_build-mutect2-annotated.vcf.gz</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">cnv_reference</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">purecn_normaldb</span><span class="pi">:</span> <span class="s" style="color: #d14;">/path/ton/config/normalDB_hg38.rds</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">purecn_mapping_bias</span><span class="pi">:</span> <span class="s" style="color: #d14;">/path/ton/config/mapping_bias_hg38.rds</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">metadata</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;">phenotype</span><span class="pi">:</span> <span class="s" style="color: #d14;">tumor</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#d4a01618e69ec23258bcf7f41f3a10f71f40ddee"><strong>config/vcfanno/GRCh37-gemini.conf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="conf"><span class="n" style="color: #333;">file</span>=<span class="s2" style="color: #d14;">"variation/exac.vcf.gz"</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"AC_Adj"</span>, <span class="s2" style="color: #d14;">"AN_Adj"</span>, <span class="s2" style="color: #d14;">"AC_AFR"</span>, <span class="s2" style="color: #d14;">"AN_AFR"</span>, <span class="s2" style="color: #d14;">"AC_AMR"</span>, <span class="s2" style="color: #d14;">"AN_AMR"</span>, <span class="s2" style="color: #d14;">"AC_EAS"</span>, <span class="s2" style="color: #d14;">"AN_EAS"</span>, <span class="s2" style="color: #d14;">"AC_FIN"</span>, <span class="s2" style="color: #d14;">"AN_FIN"</span>, <span class="s2" style="color: #d14;">"AC_NFE"</span>, <span class="s2" style="color: #d14;">"AN_NFE"</span>, <span class="s2" style="color: #d14;">"AC_OTH"</span>, <span class="s2" style="color: #d14;">"AN_OTH"</span>, <span class="s2" style="color: #d14;">"AC_SAS"</span>, <span class="s2" style="color: #d14;">"AN_SAS"</span>, <span class="s2" style="color: #d14;">"AC_Het"</span>, <span class="s2" style="color: #d14;">"AC_Hom"</span>]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"ac_exac_all"</span>, <span class="s2" style="color: #d14;">"an_exac_all"</span>, <span class="s2" style="color: #d14;">"ac_adj_exac_afr"</span>, <span class="s2" style="color: #d14;">"an_adj_exac_afr"</span>, <span class="s2" style="color: #d14;">"ac_adj_exac_amr"</span>, <span class="s2" style="color: #d14;">"an_adj_exac_amr"</span>, <span class="s2" style="color: #d14;">"ac_adj_exac_eas"</span>, <span class="s2" style="color: #d14;">"an_adj_exac_eas"</span>, <span class="s2" style="color: #d14;">"ac_adj_exac_fin"</span>, <span class="s2" style="color: #d14;">"an_adj_exac_fin"</span>, <span class="s2" style="color: #d14;">"ac_adj_exac_nfe"</span>, <span class="s2" style="color: #d14;">"an_adj_exac_nfe"</span>, <span class="s2" style="color: #d14;">"ac_adj_exac_oth"</span>, <span class="s2" style="color: #d14;">"an_adj_exac_oth"</span>, <span class="s2" style="color: #d14;">"ac_adj_exac_sas"</span>, <span class="s2" style="color: #d14;">"an_adj_exac_sas"</span>, <span class="s2" style="color: #d14;">"num_exac_Het"</span>, <span class="s2" style="color: #d14;">"num_exac_Hom"</span>]</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"max"</span>, <span class="s2" style="color: #d14;">"<span class="idiff left">self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff right">] </span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"max"</span>, <span class="s2" style="color: #d14;">"<span class="idiff left">max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"max"</span></span><span class="idiff right">]</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="conf">[[<span class="n" style="color: #333;">annotation</span>]]</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="conf"><span class="n" style="color: #333;">file</span>=<span class="s2" style="color: #d14;">"variation/gnomad_exome.vcf.gz"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -16,11 +16,12 @@ fields=["EA_AC", "AA_AC", "TAC"]</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"af_esp_ea_float"</span>, <span class="s2" style="color: #d14;">"af_esp_aa_float"</span>, <span class="s2" style="color: #d14;">"af_esp_all_float"</span>]</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"lua:ratio(vals)"</span>, <span class="s2" style="color: #d14;">"lua:ratio(vals)"</span>, <span class="s2" style="color: #d14;">"lua:ratio(vals)"</span>]</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="conf"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="conf">[[<span class="n" style="color: #333;">annotation</span>]]</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="conf"><span class="n" style="color: #333;">file</span>=<span class="s2" style="color: #d14;">"variation/dbsnp<span class="idiff left right">-151</span>.vcf.gz"</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"ID"</span>]</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"rs_id<span class="idiff left right">s</span>"</span>]</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"<span class="idiff left right">concat</span>"</span>]</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="conf"><span class="n" style="color: #333;">file</span>=<span class="s2" style="color: #d14;">"variation/dbsnp.vcf.gz"</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"ID"</span><span class="idiff left">, </span><span class="s2" style="color: #d14;"><span class="idiff">"CAF"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"FREQ"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"ID"</span></span>]</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"rs_id<span class="idiff left">"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"CAF"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"FREQ"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"DB</span>"</span>]</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"<span class="idiff left">first"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"flag</span>"</span>]</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="conf">[[<span class="n" style="color: #333;">annotation</span>]]</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="conf"><span class="n" style="color: #333;">file</span>=<span class="s2" style="color: #d14;">"variation/1000g.vcf.gz"</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">@@ -28,12 +29,11 @@ fields=["AMR_AF", "EAS_AF", "SAS_AF", "AFR_AF", "EUR_AF", "AF"]</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"af_1kg_amr"</span>, <span class="s2" style="color: #d14;">"af_1kg_eas"</span>, <span class="s2" style="color: #d14;">"af_1kg_sas"</span>, <span class="s2" style="color: #d14;">"af_1kg_afr"</span>, <span class="s2" style="color: #d14;">"af_1kg_eur"</span>, <span class="s2" style="color: #d14;">"af_1kg_all"</span>]</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"max"</span>, <span class="s2" style="color: #d14;">"max"</span>, <span class="s2" style="color: #d14;">"max"</span>, <span class="s2" style="color: #d14;">"max"</span>, <span class="s2" style="color: #d14;">"max"</span>, <span class="s2" style="color: #d14;">"max"</span>]</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="conf"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="conf">[[<span class="n" style="color: #333;">annotation</span>]]</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="conf"><span class="n" style="color: #333;">file</span>=<span class="s2" style="color: #d14;">"variation/clinvar.vcf.gz"</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"CLNSIG"</span>, <span class="s2" style="color: #d14;">"CLNDBN"</span>]</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"clinvar_sig"</span>, <span class="s2" style="color: #d14;">"clinvar_disease_name"</span>]</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"self"</span>, <span class="s2" style="color: #d14;">"self"</span>]</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"CLNSIG"</span>, <span class="s2" style="color: #d14;">"CLNDBN"</span><span class="idiff left">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"GENEINFO"</span></span>]</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"clinvar_sig"</span>, <span class="s2" style="color: #d14;">"clinvar_disease_name"</span><span class="idiff left">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"clinvar_geneinfo"</span></span>]</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"self"</span>, <span class="s2" style="color: #d14;">"self"</span><span class="idiff left">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"self"</span></span>]</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># calculate allele frequencies for all populations.</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="conf">[[<span class="n" style="color: #333;">postannotation</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">@@ -84,7 +84,6 @@ name="af_adj_exac_sas"</td>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="conf"><span class="n" style="color: #333;">op</span>=<span class="s2" style="color: #d14;">"div2"</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="conf"><span class="n" style="color: #333;">type</span>=<span class="s2" style="color: #d14;">"Float"</span></span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="conf"></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="conf"></span>
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88
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="conf">[[<span class="n" style="color: #333;">postannotation</span>]]</span>
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89
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s1" style="color: #d14;">'af_adj_exac_afr'</span>, <span class="s1" style="color: #d14;">'af_adj_exac_amr'</span>, <span class="s1" style="color: #d14;">'af_adj_exac_eas'</span>, <span class="s1" style="color: #d14;">'af_adj_exac_fin'</span>, <span class="s1" style="color: #d14;">'af_adj_exac_nfe'</span>, <span class="s1" style="color: #d14;">'af_adj_exac_oth'</span>, <span class="s1" style="color: #d14;">'af_adj_exac_sas'</span>, <span class="s2" style="color: #d14;">"af_esp_ea"</span>, <span class="s2" style="color: #d14;">"af_esp_aa"</span>, <span class="s2" style="color: #d14;">"af_esp_all"</span>, <span class="s2" style="color: #d14;">"af_1kg_amr"</span>, <span class="s2" style="color: #d14;">"af_1kg_eas"</span>, <span class="s2" style="color: #d14;">"af_1kg_sas"</span>, <span class="s2" style="color: #d14;">"af_1kg_afr"</span>, <span class="s2" style="color: #d14;">"af_1kg_eur"</span>, <span class="s2" style="color: #d14;">"af_1kg_all"</span>]</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="conf"><span class="n" style="color: #333;">op</span>=<span class="s2" style="color: #d14;">"max"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,8 +102,8 @@ op="lua:check_population_aaf(max_aaf_all, 0.01)"</td>
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103
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="conf"><span class="n" style="color: #333;">name</span>=<span class="s2" style="color: #d14;">"DB"</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="conf"><span class="n" style="color: #333;">type</span>=<span class="s2" style="color: #d14;">"Flag"</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="conf"></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="conf">[[<span class="n" style="color: #333;">annotation</span>]]</span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="conf"><span class="n" style="color: #333;"><span class="idiff left">file</span></span><span class="idiff">=</span><span class="s2" style="color: #d14;"><span class="idiff right">"variation/cosmic.vcf.gz</span>"</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"ID"</span>]</span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="conf"><span class="n" style="color: #333;"><span class="idiff left">names</span></span><span class="idiff">=[</span><span class="s2" style="color: #d14;"><span class="idiff">"cosmic_ids"</span></span><span class="idiff right">]</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="conf"><span class="n" style="color: #333;"><span class="idiff left">ops</span></span><span class="idiff">=[</span><span class="s2" style="color: #d14;"><span class="idiff">"uniq"</span></span><span class="idiff right">]</span></span></pre>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="conf">[[<span class="n" style="color: #333;"><span class="idiff left right">post</span>annotation</span>]]</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="conf"><span class="n" style="color: #333;"><span class="idiff left">name</span></span><span class="idiff">=</span><span class="s2" style="color: #d14;"><span class="idiff right">"ID</span>"</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"<span class="idiff left">rs_id"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"</span>ID"</span>]</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="conf"><span class="n" style="color: #333;"><span class="idiff left">op</span></span><span class="idiff">=</span><span class="s2" style="color: #d14;"><span class="idiff right">"setid"</span></span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="conf"><span class="n" style="color: #333;"><span class="idiff left">type</span></span><span class="idiff">=</span><span class="s2" style="color: #d14;"><span class="idiff right">"String"</span></span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#062859ad0e9ca8b80ef940d89d80463771aa419e"><strong>config/vcfanno/hg38-gemini.conf</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">@@ -20,17 +20,17 @@ ops=["lua:ratio(vals)", "lua:ratio(vals)", "lua:ratio(vals)"]</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="conf">[[<span class="n" style="color: #333;">annotation</span>]]</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="conf"><span class="n" style="color: #333;">file</span>=<span class="s2" style="color: #d14;">"variation/dbsnp<span class="idiff left right">-153</span>.vcf.gz"</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"ID"</span>]</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"rs_id<span class="idiff left right">s</span>"</span>]</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"<span class="idiff left right">concat</span>"</span>]</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="conf"><span class="n" style="color: #333;">file</span>=<span class="s2" style="color: #d14;">"variation/dbsnp.vcf.gz"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"ID"</span><span class="idiff left">, </span><span class="s2" style="color: #d14;"><span class="idiff">"CAF"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"FREQ"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"ID"</span></span>]</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"rs_id<span class="idiff left">"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"CAF"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"FREQ"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"ID</span>"</span>]</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"<span class="idiff left">first"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff">"self"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"flag</span>"</span>]</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="conf">[[<span class="n" style="color: #333;">annotation</span>]]</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="conf"><span class="n" style="color: #333;">file</span>=<span class="s2" style="color: #d14;">"variation/clinvar.vcf.gz"</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"CLNSIG"</span>, <span class="s2" style="color: #d14;">"CLNDBN"</span>]</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"clinvar_sig"</span>, <span class="s2" style="color: #d14;">"clinvar_disease_name"</span>]</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"self"</span>, <span class="s2" style="color: #d14;">"self"</span>]</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"CLNSIG"</span>, <span class="s2" style="color: #d14;">"CLNDBN"</span><span class="idiff left">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"GENEINFO"</span></span>]</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"clinvar_sig"</span>, <span class="s2" style="color: #d14;">"clinvar_disease_name"</span><span class="idiff left">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"clinvar_geneinfo"</span></span>]</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"self"</span>, <span class="s2" style="color: #d14;">"self"</span><span class="idiff left">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"self"</span></span>]</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># calculate allele frequencies for all populations.</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="conf">[[<span class="n" style="color: #333;">postannotation</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">@@ -99,3 +99,9 @@ fields=["max_aaf_all"]</td>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="conf"><span class="n" style="color: #333;">op</span>=<span class="s2" style="color: #d14;">"lua:check_population_aaf(max_aaf_all, 0.01)"</span></span>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="conf"><span class="n" style="color: #333;">name</span>=<span class="s2" style="color: #d14;">"DB"</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="conf"><span class="n" style="color: #333;">type</span>=<span class="s2" style="color: #d14;">"Flag"</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="conf"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="conf">[[<span class="n" style="color: #333;">postannotation</span>]]</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="conf"><span class="n" style="color: #333;">name</span>=<span class="s2" style="color: #d14;">"ID"</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"rs_id"</span>, <span class="s2" style="color: #d14;">"ID"</span>]</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="conf"><span class="n" style="color: #333;">op</span>=<span class="s2" style="color: #d14;">"setid"</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="conf"><span class="n" style="color: #333;">type</span>=<span class="s2" style="color: #d14;">"String"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#90758652aa44d7aee266bd0d90a2fe01bf23ac55"><strong>config/vcfanno/somatic.conf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,29 +2,14 @@</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># Requires a manual installation of COSMIC</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># https://bcbio-nextgen.readthedocs.io/en/latest/contents/installation.html?highlight=cosmic#customizing-data-installation </span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="conf"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="conf">[[<span class="n" style="color: #333;">annotation</span>]]</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="conf"><span class="n" style="color: #333;">file</span>=<span class="s2" style="color: #d14;">"variation/dbsnp-153.vcf.gz"</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"ID"</span>, <span class="s2" style="color: #d14;">"CAF"</span>, <span class="s2" style="color: #d14;">"ID"</span>]</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"rs_id"</span>, <span class="s2" style="color: #d14;">"CAF"</span>, <span class="s2" style="color: #d14;">"DB"</span>]</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"first"</span>, <span class="s2" style="color: #d14;">"first"</span>, <span class="s2" style="color: #d14;">"flag"</span>]</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="conf">[[<span class="n" style="color: #333;">annotation</span>]]</span>
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12
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="conf"><span class="n" style="color: #333;">file</span>=<span class="s2" style="color: #d14;">"variation/cosmic.vcf.gz"</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"ID"</span>, <span class="s2" style="color: #d14;">"CNT"</span>, <span class="s2" style="color: #d14;">"AA"</span>, <span class="s2" style="color: #d14;">"CDS"</span>, <span class="s2" style="color: #d14;">"GENE"</span>]</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"cosmic_id"</span>, <span class="s2" style="color: #d14;">"CNT"</span>, <span class="s2" style="color: #d14;">"AA"</span>, <span class="s2" style="color: #d14;">"CDS"</span>, <span class="s2" style="color: #d14;">"GENE"</span>]</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"first"</span>, <span class="s2" style="color: #d14;">"first"</span>, <span class="s2" style="color: #d14;">"first"</span>, <span class="s2" style="color: #d14;">"first"</span>, <span class="s2" style="color: #d14;">"first"</span>]</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="conf"></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="conf">[[<span class="n" style="color: #333;">annotation</span>]]</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="conf"><span class="n" style="color: #333;">file</span>=<span class="s2" style="color: #d14;">"variation/clinvar.vcf.gz"</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"CLNSIG"</span>, <span class="s2" style="color: #d14;">"GENEINFO"</span>]</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"first"</span>, <span class="s2" style="color: #d14;">"first"</span>]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"ID"</span>]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="conf"><span class="n" style="color: #333;">names</span>=[<span class="s2" style="color: #d14;">"cosmic_id"</span>]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="conf"><span class="n" style="color: #333;">ops</span>=[<span class="s2" style="color: #d14;">"uniq"</span>]</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="conf"></span>
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22
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="conf">[[<span class="n" style="color: #333;">postannotation</span>]]</span>
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23
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="conf"><span class="n" style="color: #333;">name</span>=<span class="s2" style="color: #d14;">"ID"</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"<span class="idiff left">rs_id"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"cosmic</span>_id"</span>, <span class="s2" style="color: #d14;">"ID"</span>]</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"<span class="idiff left">cosmic_id"</span></span><span class="idiff">, </span><span class="s2" style="color: #d14;"><span class="idiff right">"rs</span>_id"</span>, <span class="s2" style="color: #d14;">"ID"</span>]</span>
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25
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="conf"><span class="n" style="color: #333;">op</span>=<span class="s2" style="color: #d14;">"setid"</span></span>
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26
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="conf"><span class="n" style="color: #333;">type</span>=<span class="s2" style="color: #d14;">"String"</span></span></pre>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="conf"></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="conf">[[<span class="n" style="color: #333;">postannotation</span>]]</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="conf"><span class="n" style="color: #333;">fields</span>=[<span class="s2" style="color: #d14;">"rs_id"</span>, <span class="s2" style="color: #d14;">"cosmic_id"</span>]</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="conf"><span class="n" style="color: #333;">op</span>=<span class="s2" style="color: #d14;">"delete"</span></span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Bulk RNA-seq</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">Bulk RNA-seq pipeline in bcbio:</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">-</span> aligns reads with STAR (2pass), or hisat2 vs genome and transcriptome references (human, mouse, custom references);</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">-</span> quantifies expression counts with salmon, kallisto;</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">-</span> runs quality control;</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">-</span> calculates TPM with tximport;</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">-</span> detects rusions with arriba, pizzly;</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">-</span> creates a SummarizedExperiment object for downstream analysis in R;</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">-</span> calls variants with gatk or with vardict;</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">-</span> supports <span class="p">[</span><span class="nv" style="color: #008080;">spike-in</span><span class="p">](</span><span class="sx" style="color: #d14;">https://en.wikipedia.org/wiki/RNA_spike-in</span><span class="p">)</span> calibration</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Workflow</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown">This example <span class="idiff left right">aligns and creates count files for use with downstream analyses using a subset of the SEQC data</span> from the <span class="p">[</span><span class="nv" style="color: #008080;">FDA's Sequencing Quality Control project</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.fdaseqc.org/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">This example <span class="idiff left right">processes 6 RNA-seq samples</span> from the <span class="p">[</span><span class="nv" style="color: #008080;">FDA's Sequencing Quality Control project</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.fdaseqc.org/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 1. Install STAR index</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 1. Install STAR index<span class="idiff left right"> (if there is no STAR in the current bcbio installation)</span></span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown">bcbio_nextgen.py upgrade <span class="nt" style="color: #000080;">-u</span> skip <span class="nt" style="color: #000080;">--genomes</span> hg38 <span class="nt" style="color: #000080;">--aligners</span> star <span class="nt" style="color: #000080;">--cores</span> 10</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><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">@@ -20,7 +30,7 @@ Step 2 in detail:</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### 2.1 Create input directory and download fastq files</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> input</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="idiff left right">seqc/</span>input</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### 2.2 Download a template yaml file describing RNA-seq analysis</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">@@ -35,20 +45,26 @@ details:</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">analysis</span><span class="pi">:</span> <span class="s" style="color: #d14;">RNA-seq</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"> <span class="na" style="color: #008080;">genome_build</span><span class="pi">:</span> <span class="s" style="color: #d14;">hg38</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"> <span class="na" style="color: #008080;">algorithm</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"> <span class="na" style="color: #008080;">quality_format</span><span class="pi">:</span> <span class="s" style="color: #d14;">standard</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"> <span class="na" style="color: #008080;">aligner</span><span class="pi">:</span> <span class="s" style="color: #d14;">star</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"> <span class="na" style="color: #008080;">strandedness</span><span class="pi">:</span> <span class="s" style="color: #d14;">unstranded</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"><span class="na" style="color: #008080;">upload</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"> <span class="na" style="color: #008080;">dir</span><span class="pi">:</span> <span class="s" style="color: #d14;">../final</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"><span class="na" style="color: #008080;">resources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"> <span class="na" style="color: #008080;">star</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"> <span class="na" style="color: #008080;">cores</span><span class="pi">:</span> <span class="m" style="color: #099;">10</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"> <span class="na" style="color: #008080;">memory</span><span class="pi">:</span> <span class="s" style="color: #d14;">10G</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### 2.3 Download fastq files into input dir</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>input</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span><span class="idiff left right">seqc/</span>input</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"><span class="k" style="font-weight: 600;">for </span>SAMPLE <span class="k" style="font-weight: 600;">in </span>SRR950078 SRR950079 SRR950080 SRR950081 SRR950082 SRR950083</span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"><span class="k" style="font-weight: 600;">do </span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"><span class="k" style="font-weight: 600;"> </span>wget <span class="nt" style="color: #000080;">-c</span> <span class="nt" style="color: #000080;">-O</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>_1.fastq.gz</span>
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50
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"> wget <span class="nt" style="color: #000080;">-c</span> <span class="nt" style="color: #000080;">-O</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE</span><span class="k" style="font-weight: 600;">}</span>_2.fastq.gz</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd</span> ../../</span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### 2.4 Prepare a sample sheet</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,20 +81,19 @@ SRR950080,UHRR_rep2,UHRR</td>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown">SRR950081,HBRR_rep2,HBRR</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown">SRR950082,UHRR_rep3,UHRR</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown">SRR950083,HBRR_rep3,HBRR</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="markdown">SRR950084,UHRR_rep4,UHRR</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### 2.5 Generate yaml config file for analysis</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown">project.yaml = template.yaml x sample_sheet.csv</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="markdown">cd ../</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="markdown">bcbio_nextgen.py -w template rnaseq-seqc.yaml input/seqc.csv input</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown">bcbio_nextgen.py -w template rnaseq-seqc.yaml seqc.csv seqc/input/*.gz</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown">In the result you should see a folder structure:</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown">seqc</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown">|---config</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown">|---input</span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown">|---final</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown">|---work</span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,8 +125,6 @@ ipython: `sbatch bcbio.sh`:</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown">bcbio_nextgen.py ../config/seqc.yaml <span class="nt" style="color: #000080;">-n</span> 72 <span class="nt" style="color: #000080;">-t</span> ipython <span class="nt" style="color: #000080;">-s</span> slurm <span class="nt" style="color: #000080;">-q</span> medium <span class="nt" style="color: #000080;">-r</span> <span class="nv" style="color: #008080;">t</span><span class="o" style="font-weight: 600;">=</span>0-72:00 <span class="nt" style="color: #000080;">-r</span> <span class="nv" style="color: #008080;">conmem</span><span class="o" style="font-weight: 600;">=</span>20 <span class="nt" style="color: #000080;">--timeout</span> 3000 <span class="nt" style="color: #000080;">--tag</span> <span class="s2" style="color: #d14;">"rna"</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="markdown">This will run a full scale RNAseq experiment using STAR as the aligner and will take a long time to finish on a single machine. At the end it will output counts, Cufflinks quantitation and a set of QC results about each lane. If you have a cluster you can <span class="p">[</span><span class="nv" style="color: #008080;">parallelize it</span><span class="p">](</span><span class="sx" style="color: #d14;">parallel</span><span class="p">)</span> to speed it up considerably.</span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Parameters</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`transcript_assembler`</span> If set, will assemble novel genes and transcripts and merge the results into the known annotation. Can have multiple values set in a list. Supports ['cufflinks', 'stringtie'].</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">@@ -119,9 +132,9 @@ This will run a full scale RNAseq experiment using STAR as the aligner and will</td>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`expression_caller`</span> A list of optional expression callers to turn on. Supports ['cufflinks', 'express', 'stringtie', 'dexseq', 'kallisto']. Salmon and count based expression estimation are run by default. Sailfish is deprecated.</span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`fusion_caller`</span> A list of optional fusion callers to turn on. Supports [oncofuse, pizzly, ericscript, arriba].</span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`variantcaller`</span> Variant calling algorithm to call variants on RNA-seq data. Supports [gatk-haplotype] or [vardict].</span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`spikein_fasta`</span> A FASTA file of spike in sequences to quantitate.</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`spikein_fasta`</span> A FASTA file of spike in sequences to quantitate.<span class="idiff left right"> There are quantitated separately, so should be things you are not expecting to match anywhere to the genome or trancriptome of the species you are working with.</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`quantify_genome_alignments`</span> If set to True, run Salmon quantification using the genome alignments from STAR, when available. If STAR alignments are not available, use Salmon's SA mode with decoys.</span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`transcriptome_gtf`</span> A GTF file to use to specify transcripts which will override the bcbio-installed versions. This is used if you have an alternate transcriptome you want to quantitate. You can also use this option to add your own transcripts to a set to quantitate, just append them to your GTF file and sort it.</span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## QC and Basic DE analysis</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="markdown">By default, bcbio runs simple <span class="p">[</span><span class="nv" style="color: #008080;">R scripts</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/bcbio/bcbio-nextgen/tree/master/bcbio/scripts/R</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="markdown">To make them work, you need >1 sample, and <span class="sb" style="color: #d14;">`category`</span> in the metadata for each sample:</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">@@ -224,6 +237,26 @@ Our current recommendation is to run adapter trimming only if using the Tophat2</td>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="markdown">Salmon, which is an extremely fast alignment-free method of quantitation, is run for all experiments. Salmon can accurately quantitate the expression of genes, even ones which are hard to quantitate with other methods (see <span class="p">[</span><span class="nv" style="color: #008080;">this paper</span><span class="p">](</span><span class="sx" style="color: #d14;">https://doi.org/10.1186/s13059-015-0734-x</span><span class="p">)</span> for example for Sailfish, which performs similarly to Salmon). Salmon can also quantitate at the transcript level which can help gene-level analyses</span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="markdown">(see <span class="p">[</span><span class="nv" style="color: #008080;">this paper</span><span class="p">](</span><span class="sx" style="color: #d14;">https://doi.org/10.12688/f1000research.7563.1</span><span class="p">)</span> for example). We recommend using the Salmon quantitation rather than the counts from featureCounts to perform downstream quantification.</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">Still, we had at least two projects with initally low % mapped (STAR) at 50-70% which greatly benefited from trimming both in terms of % mapped and N mapped reads.</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="markdown">We trimmed with </span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown">bcbio.yaml:</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="markdown"><span class="p">```</span><span class="nl">yaml</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="markdown"><span class="na" style="color: #008080;">algorithm</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="markdown"> <span class="na" style="color: #008080;">trim_reads</span><span class="pi">:</span> <span class="s" style="color: #d14;">read_through</span> </span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="markdown"> <span class="na" style="color: #008080;">adapters</span><span class="pi">:</span> <span class="s" style="color: #d14;">illumina</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="markdown">or with <span class="p">[</span><span class="nv" style="color: #008080;">fastp</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/OpenGene/fastp</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="markdown">fastp <span class="nt" style="color: #000080;">-I</span> <span class="o" style="font-weight: 600;">{</span>input.R1]<span class="o" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-I</span> <span class="o" style="font-weight: 600;">{</span>input.R2<span class="o" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-o</span> <span class="o" style="font-weight: 600;">{</span>output.R1_trim_fastq<span class="o" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-O</span> <span class="o" style="font-weight: 600;">{</span>output.R2_trim_fastq<span class="o" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-h</span> <span class="o" style="font-weight: 600;">{</span>output.fastp_html<span class="o" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-x</span> <span class="nt" style="color: #000080;">-5</span> <span class="nt" style="color: #000080;">-3</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># Additional flag definitions:</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># -g trims polyG, common artifact in Illumina 2-dye sequencing chemistry (MiniSeq, NextSeq, Novaseq)</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># -x trims polyX, any other homopolymeric stretch</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># -5 sliding window 5’ quality trimming</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># -3 sliding window 3’ quality trimming</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="markdown"><span class="p">```</span></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">Although we do not recommend using the featureCounts based counts, the alignments are still useful because they give you many more quality metrics than the quasi-alignments from Salmon.</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">After a bcbio RNA-seq run there will be in the <span class="sb" style="color: #d14;">`upload`</span> directory a directory for each sample which contains a BAM file of the aligned and unaligned reads, a <span class="sb" style="color: #d14;">`salmon`</span> directory with the output of Salmon, including TPM values, and a <span class="sb" style="color: #d14;">`qc`</span> directory with plots from FastQC and qualimap.</span>
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<li id="b8ea2f27fdb24b27de13de2d32707e6af8788bda">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#b8ea2f27fdb24b27de13de2d32707e6af8788bda"><strong>docs/contents/configuration.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -181,7 +181,7 @@ sample1,sample1,batch1,normal,female,/path/to/regions.bed</td>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`picard`</span> -- Picard/GATK based cleaning. Includes read group changes, fixing of problematic reads and re-ordering chromosome order to match the reference genome. To fix misencoded input BAMs with non-standard scores, set <span class="sb" style="color: #d14;">`quality_format`</span> to <span class="sb" style="color: #d14;">`illumina`</span>.</span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`bam_sort`</span> Allow sorting of input BAMs when skipping alignment step (<span class="sb" style="color: #d14;">`aligner`</span> set to false). Options are coordinate or queryname. For additional processing through standard pipelines requires coordinate sorted inputs. The default is to not do additional sorting and assume pre-sorted BAMs.</span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`align_split_size`</span>: Increase parallelization of alignment. As of 0.9.8, bcbio will try to determine a useful parameter and you don't need to set this. If you manually set it, bcbio will respect your specification. Set to false to avoid splitting entirely. If set, this defines the number of records to feed into each independent parallel step (for example, 5000000 = 5 million reads per chunk). It converts the original inputs into bgzip grabix indexed FASTQ files, and then retrieves chunks for parallel alignment. Following alignment, it combines all chunks back into the final merged alignment file. This allows parallelization at the cost of additional work of preparing inputs and combining split outputs. The tradeoff makes sense when you have large files and lots of distributed compute. When you have fewer large multicore machines this parameter may not help speed up processing.</span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`quality_format`</span> Quality format of FASTQ or BAM inputs [standard, illumina]</span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`quality_format`</span> Quality format of FASTQ or BAM inputs [standard, illumina]<span class="idiff left">. </span><span class="sb" style="color: #d14;"><span class="idiff">`standard`</span></span><span class="idiff"> means Sanger, </span><span class="sb" style="color: #d14;"><span class="idiff">`illumina`</span></span><span class="idiff right"> means Illumina [1.3, 1.8).</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`strandedness`</span> For RNA-seq libraries, if your library is strand specific, set the appropriate flag from [unstranded, firststrand, secondstrand]. Defaults to unstranded. For dUTP marked libraries, firststrand is correct; for Scriptseq prepared libraries, secondstrand is correct.</span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`save_diskspace`</span> Remove align prepped bgzip and split BAM files after merging into final BAMs. Helps reduce space on limited filesystems during a run. <span class="sb" style="color: #d14;">`tools_off: [upload_alignment]`</span> may also be useful in conjunction with this. <span class="sb" style="color: #d14;">`[false, true]`</span></span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -513,6 +513,10 @@ To manually make genomes available to bcbio-nextgen, edit the individual `.loc`</td>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="markdown">To remove a reference genome, delete its directory <span class="sb" style="color: #d14;">`bcbio/genomes/species/reference`</span> and remove all the records corresponding to that genome from <span class="sb" style="color: #d14;">`bcbio/galaxy/tool-data/*.loc`</span> files.</span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="markdown"><span class="sb" style="color: #d14;">`genomes/Hsapiens/hg38/seq/hg38-resources.yaml`</span> specifies relative locations of the resources. To determine the absolute path, bcbio fetches a value</span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="markdown">from <span class="sb" style="color: #d14;">`bcbio/galaxy/tool-data/sam_fa_indices.loc`</span> and uses it is a basedir for all resources. If there are several installations of bcbio <span class="sb" style="color: #d14;">`data`</span>,</span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="markdown">it is important to have separate <span class="sb" style="color: #d14;">`tool-data`</span> as well.</span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Adding custom genomes</span></span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="markdown"></span>
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518
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">bcbio_setup_genome.py</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/bcbio/bcbio-nextgen/blob/master/scripts/bcbio_setup_genome.py</span><span class="p">)</span> installs a custom genome for variant and bulk-RNA-seq analyses and updates the configuration files. </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); 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="580" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -576,7 +580,7 @@ For adding an organism not present in snpEff, please see this [mailing list disc</td>
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Download data from SRA</span></span>
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="markdown"></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="markdown">Use SRA toolkit <span class="p">[</span><span class="nv" style="color: #008080;">prefetch/fastq-dump</span><span class="p">](</span><span class="sx" style="color: #d14;">https://wiki.rc.hms.harvard.edu/<span class="idiff left right">display/O2/Aspera+to+download+NCBI+SRA+data</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="markdown">Use SRA toolkit <span class="p">[</span><span class="nv" style="color: #008080;">prefetch/fastq-dump</span><span class="p">](</span><span class="sx" style="color: #d14;">https://wiki.rc.hms.harvard.edu/<span class="idiff left right">pages/viewpage.action?pageId=42402938</span></span><span class="p">)</span></span>
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580
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584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="markdown"></span>
</pre>
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581
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Upload</span></span>
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582
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="markdown"></span>
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<li id="83f344ca0b114299c310d87b9ef098903138d93e">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#83f344ca0b114299c310d87b9ef098903138d93e"><strong>docs/contents/installation.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -183,14 +183,14 @@ By default, bcbio will install data files for `variation`, `rnaseq` and `smallrn</td>
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`ericscript`</span> -- Database for <span class="p">[</span><span class="nv" style="color: #008080;">EricScript</span><span class="p">](</span><span class="sx" style="color: #d14;">https://sites.google.com/site/bioericscript/</span><span class="p">)</span>, based gene fusion detection. Supports hg38, hg19 and GRCh37.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`TOPMed`</span> -- <span class="p">[</span><span class="nv" style="color: #008080;">TOPMed</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.nhlbiwgs.org</span><span class="p">)</span> Allele frequencies for whole genome variants from heart, lung, blood and sleep disorders. Supports hg38, hg19 and GRCh37.</span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="markdown"></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="markdown">For somatic analyses, bcbio includes <span class="p">[</span><span class="nv" style="color: #008080;">COSMIC</span><span class="p">](</span><span class="sx" style="color: #d14;">https://cancer.sanger.ac.uk/cosmic</span><span class="p">)</span> v68 for hg19 and GRCh37 only. Due to license restrictions, we cannot include updated versions of</span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="markdown">this dataset and hg38 support with the installer. To prepare these datasets yourself you can use <span class="p">[</span><span class="nv" style="color: #008080;">a utility script shipped with cloudbiolinux</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/chapmanb/cloudbiolinux/blob/master/utils/prepare_cosmic.py</span><span class="p">)</span> that downloads, sorts and merges the VCFs, then copies into your bcbio installation:</span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="markdown">For somatic analyses, bcbio includes <span class="p">[</span><span class="nv" style="color: #008080;">COSMIC</span><span class="p">](</span><span class="sx" style="color: #d14;">https://cancer.sanger.ac.uk/cosmic</span><span class="p">)</span> v68 for hg19 and GRCh37 only. Due to license restrictions, we cannot include updated versions of this dataset and hg38 support with the installer. To prepare these datasets yourself you can use <span class="p">[</span><span class="nv" style="color: #008080;">a utility script shipped with cloudbiolinux</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/chapmanb/cloudbiolinux/blob/master/utils/prepare_cosmic.py</span><span class="p">)</span> that downloads, sorts and merges the VCFs, then copies into your bcbio installation:</span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="markdown"><span class="p">```</span><span class="nl">shell</span></span>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">COSMIC_USER</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"you@example.org"</span></span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">COSMIC_PASS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"your_cosmic_password"</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="markdown">bcbio_python prepare_cosmic.py 89 /path/to/bcbio</span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="markdown"><span class="sb" style="color: #d14;">`/path/to/bcbio/`</span> here is the directory one up from the <span class="sb" style="color: #d14;">`genomes`</span> directory.</span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="markdown"><span class="sb" style="color: #d14;">`/path/to/bcbio/`</span> here is the directory one up from the <span class="sb" style="color: #d14;">`genomes`</span> directory. The script removes variants marked as <span class="sb" style="color: #d14;">`SNP`</span> in COSMIC, i.e. leaving only somatic variants. From version a minor portion of variants gets re-classified, for example: 3,779 variants were SNPs in cosmic-90 and became mutations in cosmic-92,</span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="markdown">656 variants were mutations in cosmic-90 and became SNPs in cosmic-92.</span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Extra software</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="markdown"></span>
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<li id="d780222435a775b157cca2d5946cddc237dd74d7">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#d780222435a775b157cca2d5946cddc237dd74d7"><strong>docs/contents/purecn.md</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">@@ -90,7 +90,11 @@ mv sample1_T_FFPE.bam sample2_T_FFPE ton/input/</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 2. Create purecn_ton_template.yaml:</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown">wget https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/templates/purecn_ton.yaml</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"><span class="p">```</span><span class="nl">yaml</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"><span class="na" style="color: #008080;">details</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">analysis</span><span class="pi">:</span> <span class="s" style="color: #d14;">variant2</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown"> <span class="na" style="color: #008080;">genome_build</span><span class="pi">:</span> <span class="s" style="color: #d14;">hg38</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#b1655f936472b3a6a6a310218f78e1d19987454b"><strong>requirements-conda.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">bcbio-nextgen=1.2.<span class="idiff left right">4</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bcbio-nextgen=1.2.<span class="idiff left right">5</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#19359a61ae2446b51b549167b014da2fcf265768"><strong>requirements.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/bcbio-nextgen" rel="nofollow noreferrer noopener" target="_blank">bcbio-nextgen</a>==1.2.<span class="idiff left right">4</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/bcbio-nextgen" rel="nofollow noreferrer noopener" target="_blank">bcbio-nextgen</a>==1.2.<span class="idiff left right">5</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#bacc76312ae1e30f71298a0e5abf86c8e5dbec70"><strong>scripts/bcbio_setup_genome.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">@@ -221,25 +221,26 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC222" 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;">"-c"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--cores"</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;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC223" 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;">"number of cores to use"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC224" 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;">"-f"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--fasta"</span><span class="p">,</span> <span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FASTA file of the genome."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC224" 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;">"--gff3"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"File is a GFF3 file."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC228" 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;">"-g"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--gtf"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC229" 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;">"GTF file of the transcriptome"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC230" 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;">"-n"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--name"</span><span class="p">,</span> <span class="n" style="color: #333;">required</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="LC231" 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;">"Name of organism, for example Hsapiens."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">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;">"-b"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--build"</span><span class="p">,</span> <span class="n" style="color: #333;">required</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="LC233" 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;">"Build of genome, for example hg19."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC226" 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;">"-i"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--indexes"</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">SUPPORTED_INDEXES</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"*"</span><span class="p">,</span></span>
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235
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"seq"</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;">"Space separated list of indexes to make"</span><span class="p">)</span></span>
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236
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228
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<pre style="margin: 0;"> <span id="LC228" 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;">"--ercc"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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237
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<td class="diff-line-num new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
229
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<pre style="margin: 0;"> <span id="LC229" 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;">"Add ERCC spike-ins."</span><span class="p">)</span></span>
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238
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230
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<pre style="margin: 0;"> <span id="LC230" 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;">"--mirbase"</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;">"species in mirbase for smallRNAseq data."</span><span class="p">)</span></span>
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239
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<td class="diff-line-num new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
231
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<pre style="margin: 0;"> <span id="LC231" 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;">"--srna_gtf"</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;">"gtf to use for smallRNAseq data."</span><span class="p">)</span></span>
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240
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="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;">"--buildversion"</span><span class="p">,</span> <span class="n" style="color: #333;">required</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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241
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"String describing build of genome used. Examples: "</span></span>
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242
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="s" style="color: #d14;">"Ensembl_94, EnsemblMetazoa_94, Flybase_21, etc"</span><span class="p">))</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">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;">'required named arguments'</span><span class="p">)</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--buildversion"</span><span class="p">,</span> <span class="n" style="color: #333;">required</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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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"String describing build of genome used. Examples: "</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="s" style="color: #d14;">"Ensembl_94, EnsemblMetazoa_94, Flybase_21, etc"</span><span class="p">))</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-f"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--fasta"</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
237
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<pre style="margin: 0;">+<span id="LC237" 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;">"FASTA file of the genome."</span><span class="p">)</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-g"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--gtf"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
239
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<pre style="margin: 0;">+<span id="LC239" 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;">"GTF file of the transcriptome"</span><span class="p">)</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-n"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--name"</span><span class="p">,</span> <span class="n" style="color: #333;">required</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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241
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<pre style="margin: 0;">+<span id="LC241" 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;">"Name of organism, for example Hsapiens."</span><span class="p">)</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-b"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--build"</span><span class="p">,</span> <span class="n" style="color: #333;">required</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="LC243" 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;">"Build of genome, for example hg19."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC244" 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>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if not all([args.mirbase, args.srna_gtf]) and any([args.mirbase, args.srna_gtf]):</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># raise ValueError("--mirbase and --srna_gtf both need a value.")</span></span>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/5c8848abe4fd3d8b9864a6b79451c82111cfbb92#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ import subprocess</td>
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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;">setuptools</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.2.<span class="idiff left right">5</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC10" 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;">'1.2.<span class="idiff left right">6</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># add bcbio version number and git commit hash of the current revision to version.py</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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