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<h1 class="title toc-ignore">CGPBox Pipeline</h1>
<h4 class="author"><em><hr /></em></h4>
</div>
<div id="workflow-graph" class="section level1">
<h1>Workflow Graph</h1>
<p><a href="https://github.com/cancerit/cgpbox" class="uri">https://github.com/cancerit/cgpbox</a></p>
<p>This is a repackaging of the cgpbox pipeline to allow for parellization via the rabix executor and descriptions of the tools included by commmon workflow language.</p>
<p>
<img src="images/cwlbox_wf_graph.png" width="1000" />
</p>
<p><br><br></p>
</div>
<div id="descriptions-of-individual-tools" class="section level1">
<h1>Descriptions of Individual Tools</h1>
<div id="cgp-bam-stats" class="section level2 tabset tabset-fade tabset-tabs">
<h2>1. CGP Bam Stats</h2>
<hr>
<p>Generates useful stats on the wildtype and mutant tumour bams that will be used in the pipeline.</p>
<div id="base-command" class="section level3">
<h3>base command</h3>
<div class="sourceCode"><pre class="sourceCode sh"><code class="sourceCode bash">
<span class="kw">bam_stats</span> -i <span class="ot">$BAM_MT_TMP</span> -o <span class="ot">$BAM_MT_TMP</span>.bas</code></pre></div>
<p><br><br><br><br></p>
</div>
<div id="docker" class="section level3">
<h3>docker</h3>
<p>The docker conatiner is</p>
<p><code>cgrlab/cgpbox_dev:develop</code></p>
</div>
<div id="app-ports" class="section level3 tabset tabset-fade tabset-tabs">
<h3>App ports</h3>
<div id="inputs" class="section level4">
<h4>Inputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">inputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"bam"</span>, <span class="dt">label =</span> <span class="st">"bam"</span>, <span class="dt">description =</span> <span class="st">"either wildtype or tumour bam"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".bai"</span>), <span class="dt">prefix =</span> <span class="st">"-i"</span>)
)</code></pre></div>
</div>
<div id="arguments" class="section level4">
<h4>arguments</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">arguments =<span class="st"> </span>(<span class="kw">CCBList</span>(
<span class="kw">CommandLineBinding</span>(<span class="dt">position =</span> <span class="dv">2</span>, <span class="dt">prefix =</span> <span class="st">"-o"</span>, <span class="dt">valueFrom =</span> <span class="kw">list</span>(<span class="st">"{return $job.inputs.bam.name + </span><span class="ch">\"</span><span class="st">.bas</span><span class="ch">\"</span><span class="st">}"</span>)),
<span class="kw">CommandLineBinding</span>(<span class="dt">position =</span> <span class="dv">3</span>, <span class="dt">valueFrom =</span> <span class="kw">list</span>(<span class="st">"</span><span class="ch">\"</span><span class="st">&& ls -lR </span><span class="ch">\"</span><span class="st">"</span>))
))</code></pre></div>
</div>
<div id="outputs" class="section level4">
<h4>Outputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">outputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"std_out"</span>, <span class="dt">label =</span> <span class="st">"std_out"</span>,
<span class="dt">description =</span> <span class="st">"standard output"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>,
<span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span><span class="st">"</span><span class="ch">\"</span><span class="st">std.out</span><span class="ch">\"</span><span class="st">"</span>),
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"bam_statistics"</span>, <span class="dt">label =</span> <span class="st">"bam stat output"</span>,
<span class="dt">description =</span> <span class="st">"bam stat output"</span>, <span class="dt">type =</span> <span class="st">"File"</span>,
<span class="dt">inheritMetadataFrom =</span> <span class="st">"#bam"</span>, <span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">*.bas</span><span class="ch">\"</span><span class="st">"</span>))
)</code></pre></div>
</div>
</div>
<div id="define-tool-object-and-push-to-platform" class="section level3 tabset tabset-fade tabset-tabs">
<h3>Define Tool Object and Push to Platform</h3>
<div id="tool-object" class="section level4">
<h4>Tool object</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tool <-<span class="st"> </span><span class="kw">Tool</span>(
<span class="dt">id =</span> <span class="st">"bam-stats"</span>,
<span class="dt">label =</span> <span class="st">"CGP bam stats"</span>,
<span class="dt">hints =</span> <span class="kw">requirements</span>(<span class="kw">docker</span>(<span class="dt">pull =</span> <span class="st">"cgrlab/cgpbox_dev:develop"</span>), <span class="kw">cpu</span>(<span class="dv">1</span>), <span class="kw">mem</span>(<span class="dv">1000</span>)),
<span class="dt">baseCommand =</span> <span class="st">"bam_stats"</span>,
<span class="dt">stdout =</span> <span class="st">"std.out"</span>,
<span class="dt">inputs =</span> inputs,
<span class="dt">arguments =</span> arguments,
<span class="dt">outputs =</span> outputs)</code></pre></div>
</div>
<div id="push-app-to-sbg-platform" class="section level4">
<h4>Push app to sbg platform</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">project$<span class="kw">app_add</span>(<span class="st">"bam-stats"</span>, tool)</code></pre></div>
</div>
</div>
</div>
<div id="cgp-genotype-check" class="section level2 tabset tabset-fade tabset-tabs">
<h2>2. CGP Genotype Check</h2>
<hr>
<div id="base-command-1" class="section level3">
<h3>base command</h3>
<div class="sourceCode"><pre class="sourceCode sh"><code class="sourceCode bash">
<span class="kw">compareBamGenotypes.pl</span> \
-o /datastore/output/<span class="ot">$NAME_WT</span>/genotyped \
-nb <span class="ot">$BAM_WT_TMP</span> \
-j /datastore/output/<span class="ot">$NAME_WT</span>/genotyped/result.json \
-tb <span class="ot">$BAM_MT_TMP</span> \</code></pre></div>
<p><br><br><br><br></p>
</div>
<div id="docker-1" class="section level3">
<h3>docker</h3>
<p>The docker conatiner is</p>
<p><code>cgrlab/cgpbox_dev:develop</code></p>
</div>
<div id="app-ports-1" class="section level3 tabset tabset-fade tabset-tabs">
<h3>App ports</h3>
<div id="inputs-1" class="section level4">
<h4>Inputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">inputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"normal_bam"</span>, <span class="dt">label =</span> <span class="st">"normal_bam"</span>, <span class="dt">description =</span> <span class="st">"normal wildtype bam"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">prefix =</span> <span class="st">"-nb"</span>, <span class="dt">stageInput =</span> <span class="st">"link"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".bai"</span>)),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"tumour_bam"</span>, <span class="dt">label =</span> <span class="st">"tumour_bam"</span>, <span class="dt">description =</span> <span class="st">"mutant tumour bam"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">prefix =</span> <span class="st">"-tb"</span>, <span class="dt">stageInput =</span> <span class="st">"link"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".bai"</span>))
)</code></pre></div>
</div>
<div id="arguments-1" class="section level4">
<h4>arguments</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">arguments =<span class="st"> </span><span class="kw">CCBList</span>(<span class="kw">CommandLineBinding</span>(<span class="dt">position =</span> <span class="dv">99</span>, <span class="dt">valueFrom =</span> <span class="kw">list</span>(<span class="st">"</span><span class="ch">\"</span><span class="st">&& ls -lR</span><span class="ch">\"</span><span class="st">"</span>)))</code></pre></div>
</div>
<div id="outputs-1" class="section level4">
<h4>Outputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">outputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"std_out"</span>, <span class="dt">label =</span> <span class="st">"std_out"</span>,
<span class="dt">description =</span> <span class="st">"standard output"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>,
<span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">std.out</span><span class="ch">\"</span><span class="st">"</span>),
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"genotype_comparison_results"</span>, <span class="dt">label =</span> <span class="st">"genotype comparison results"</span>,
<span class="dt">description =</span> <span class="st">"genotype comarison results"</span>, <span class="dt">type =</span> <span class="st">"File"</span>,
<span class="dt">inheritMetadataFrom =</span> <span class="st">"#tumour_bam"</span>, <span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">genotype_check/*.json</span><span class="ch">\"</span><span class="st">"</span>))
)</code></pre></div>
</div>
</div>
<div id="define-tool-object-and-push-to-platform-1" class="section level3 tabset tabset-fade tabset-tabs">
<h3>Define Tool Object and Push to Platform</h3>
<div id="tool-object-1" class="section level4">
<h4>Tool object</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tool <-<span class="st"> </span><span class="kw">Tool</span>(
<span class="dt">id =</span> <span class="st">"genotype-check"</span>,
<span class="dt">label =</span> <span class="st">"compare bam genotypes"</span>,
<span class="dt">hints =</span> <span class="kw">requirements</span>(<span class="kw">docker</span>(<span class="dt">pull =</span> <span class="st">"cgrlab/cgpbox_dev:develop"</span>), <span class="kw">cpu</span>(<span class="dv">1</span>), <span class="kw">mem</span>(<span class="dv">1000</span>)),
<span class="dt">baseCommand =</span> <span class="st">"compareBamGenotypes.pl -o genotype_check -j genotype_check/genotype_check_result.json"</span>,
<span class="dt">stdout =</span> <span class="st">"std.out"</span>,
<span class="dt">inputs =</span> inputs,
<span class="dt">argument =</span> arguments,
<span class="dt">outputs =</span> outputs)</code></pre></div>
</div>
<div id="make-cwl-file" class="section level4">
<h4>Make cwl file</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">write</span>(tool$<span class="kw">toJSON</span>(<span class="dt">pretty =</span> <span class="ot">TRUE</span>), <span class="st">"genotype_check.json"</span>)</code></pre></div>
</div>
<div id="push-app-to-sbg-platform-1" class="section level4">
<h4>Push app to sbg platform</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">project$<span class="kw">app_add</span>(<span class="st">"genotype-check"</span>, tool)</code></pre></div>
</div>
</div>
</div>
<div id="verify-bams" class="section level2 tabset tabset-fade tabset-tabs">
<h2>3. Verify Bams</h2>
<hr>
<div id="base-command-2" class="section level3">
<h3>base command</h3>
<div class="sourceCode"><pre class="sourceCode sh"><code class="sourceCode bash">
<span class="kw">verifyBamHomChk.pl</span>
<span class="kw">-b</span> [bam file]
<span class="kw">-a</span> [tumour only - from ASCAT tool - called copynumber.caveman.csv ]
<span class="kw">-d</span> 25
<span class="kw">-o</span> ./
<span class="kw">-j</span> result.json</code></pre></div>
<p><br><br><br><br></p>
</div>
<div id="docker-2" class="section level3">
<h3>docker</h3>
<p>The docker conatiner is</p>
<p><code>cgrlab/cgpbox_dev:develop</code></p>
</div>
<div id="app-ports-2" class="section level3 tabset tabset-fade tabset-tabs">
<h3>App ports</h3>
<div id="inputs-2" class="section level4">
<h4>Inputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">inputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"bam"</span>, <span class="dt">label =</span> <span class="st">"bam"</span>, <span class="dt">description =</span> <span class="st">"either normal wildtype or tumour mutatantbam"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">prefix =</span> <span class="st">"-b"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".bai"</span>)),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"ascat_adjusted_copynumber_csv"</span>, <span class="dt">label =</span> <span class="st">"ascat_adjusted_copynumber_csv"</span>, <span class="dt">description =</span> <span class="st">"ascat adjusted for caveman copynumber csv"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">valueFrom =</span> <span class="kw">list</span>(<span class="st">"{if ($job.inputs.bam.metadata.sample_type == </span><span class="ch">\"</span><span class="st">Tumor</span><span class="ch">\"</span><span class="st">){return $self.path;}}"</span>), <span class="dt">prefix =</span> <span class="st">"-a"</span>)
)</code></pre></div>
</div>
<div id="arguments-2" class="section level4">
<h4>arguments</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">arguments =<span class="st"> </span><span class="kw">CCBList</span>(<span class="kw">CommandLineBinding</span>(<span class="dt">position =</span> <span class="dv">99</span>, <span class="dt">valueFrom =</span> <span class="kw">list</span>(<span class="st">"</span><span class="ch">\"</span><span class="st">&& ls -lR</span><span class="ch">\"</span><span class="st">"</span>)))</code></pre></div>
</div>
<div id="outputs-2" class="section level4">
<h4>Outputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">outputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"std_out"</span>, <span class="dt">label =</span> <span class="st">"std_out"</span>,
<span class="dt">description =</span> <span class="st">"standard output"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>,
<span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">*.{out}</span><span class="ch">\"</span><span class="st">"</span>)),
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"verify_bam_result"</span>, <span class="dt">label =</span> <span class="st">"verify_bam_results"</span>,
<span class="dt">description =</span> <span class="st">"verify bam results"</span>, <span class="dt">type =</span> <span class="st">"File"</span>,
<span class="dt">inheritMetadataFrom =</span> <span class="st">"#bam"</span>, <span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">verify_bam/verify_bam_result.json</span><span class="ch">\"</span><span class="st">"</span>))
)</code></pre></div>
</div>
</div>
<div id="define-tool-object-and-push-to-platform-2" class="section level3 tabset tabset-fade tabset-tabs">
<h3>Define Tool Object and Push to Platform</h3>
<div id="tool-object-2" class="section level4">
<h4>Tool object</h4>
<p>need to add some logic for -a adjusted copy number because it is only needed if it is the tumour sample.</p>
<pre><code>-a /datastore/output/${NAME_MT}_vs_${NAME_WT}/ascat/${NAME_MT}.copynumber.caveman.csv
arguments = CCBList(CommandLineBinding(position = 2, prefix = "-a", valueFrom = list("\"if $self.metadata.sample_type = \"Tumor\" then \""))),
{if ($job.inputs.bam.metadata.sample_type == "Tumor") {command_line_arg = "ab.copynumber.caveman.csv";} else {command_line_arg = "";} return command_line_arg}
{if ($job.inputs.bam.metadata.sampleType == "Tumor") {command_line_arg = "ab.copynumber.caveman.csv";} else {command_line_arg = "";} return command_line_arg}
</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tool <-<span class="st"> </span><span class="kw">Tool</span>(
<span class="dt">id =</span> <span class="st">"verify_bam"</span>,
<span class="dt">label =</span> <span class="st">"verify_bam"</span>,
<span class="dt">hints =</span> <span class="kw">requirements</span>(<span class="kw">docker</span>(<span class="dt">pull =</span> <span class="st">"cgrlab/cgpbox_dev:develop"</span>), <span class="kw">cpu</span>(<span class="dv">1</span>), <span class="kw">mem</span>(<span class="dv">1000</span>)),
<span class="dt">baseCommand =</span> <span class="st">"verifyBamHomChk.pl -d 25 -o verify_bam -j verify_bam/verify_bam_result.json"</span>,
<span class="dt">stdout =</span> <span class="st">"std.out"</span>,
<span class="dt">inputs =</span> inputs, <span class="dt">arguments =</span> arguments, <span class="dt">outputs =</span> outputs)</code></pre></div>
</div>
<div id="push-app-to-sbg-platform-2" class="section level4">
<h4>Push app to sbg platform</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">project$<span class="kw">app_add</span>(<span class="st">"verify_bams"</span>, tool)</code></pre></div>
</div>
</div>
</div>
<div id="ascat" class="section level2 tabset tabset-fade tabset-tabs">
<h2>4. ASCAT</h2>
<hr>
<p>Somatic copy number analysis using paired end wholegenome sequencing</p>
<p><a href="https://github.com/cancerit/ascatNgs" class="uri">https://github.com/cancerit/ascatNgs</a></p>
<div id="base-command-3" class="section level3">
<h3>base command</h3>
<div class="sourceCode"><pre class="sourceCode sh"><code class="sourceCode bash">
<span class="kw">ascat.pl</span>
<span class="kw">-t</span> [tumour bam]
<span class="kw">-n</span> [normal wildtype bam]
<span class="kw">-r</span> [genome reference]
<span class="kw">-c</span> [cpu number]
<span class="kw">-rs</span> <span class="st">'HUMAN'</span>
<span class="kw">-ra</span> GRCh37
<span class="kw">-pr</span> WGS
<span class="kw">-pl</span> ILLUMINA
<span class="kw">-sg</span> ascat_SnpGcCorrections.tsv
<span class="kw">-q</span> 20
<span class="kw">-g</span> L
<span class="kw">-o</span> ./ascat_output</code></pre></div>
</div>
<div id="prep-ascat-for-caveman" class="section level3">
<h3>Prep ASCAT for caveman</h3>
<pre><code>
&& perl -ne '@F=(split q{,}, $_)[1,2,3,4]; $F[1]-1; print join("\t",@F)."\n";' < copynumber.caveman.csv > ./normal_cn.bed && perl -ne '@F=(split q{,}, $_)[1,2,3,6]; $F[1]-1; print join("\t",@F)."\n";' < copynumber.caveman.csv > ./tumour_cn.bed
</code></pre>
<p><br><br><br><br></p>
</div>
<div id="docker-3" class="section level3">
<h3>docker</h3>
<p>The docker conatiner is</p>
<p><code>cgrlab/cgpbox_dev:develop</code></p>
</div>
<div id="app-ports-3" class="section level3 tabset tabset-fade tabset-tabs">
<h3>App ports</h3>
<div id="inputs-3" class="section level4">
<h4>Inputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">inputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"tumour_bam"</span>, <span class="dt">label =</span> <span class="st">"tumour_bam"</span>, <span class="dt">description =</span> <span class="st">"mutant tumour bam"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".bai"</span>), <span class="dt">prefix =</span> <span class="st">"-t"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"normal_bam"</span>, <span class="dt">label =</span> <span class="st">"normal_bam"</span>, <span class="dt">description =</span> <span class="st">"normal wildtype bam"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".bai"</span>), <span class="dt">prefix =</span> <span class="st">"-n"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"reference"</span>, <span class="dt">label =</span> <span class="st">"reference"</span>, <span class="dt">description =</span> <span class="st">"genome reference"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".fai"</span>), <span class="dt">prefix =</span> <span class="st">"-r"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"cgpbox_reference_files"</span>, <span class="dt">label =</span> <span class="st">"cgpbox_reference_files"</span>, <span class="dt">description =</span> <span class="st">"extracted reference files"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>, <span class="dt">stageInput =</span> <span class="st">"link"</span>)
)</code></pre></div>
</div>
<div id="arguments-3" class="section level4">
<h4>arguments</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">arguments =<span class="st"> </span><span class="kw">CCBList</span>(<span class="kw">CommandLineBinding</span>(<span class="dt">position =</span> <span class="dv">99</span>, <span class="dt">valueFrom =</span> <span class="kw">list</span>(<span class="st">"</span><span class="ch">\"</span><span class="st">&& ls -lR</span><span class="ch">\"</span><span class="st">"</span>)))</code></pre></div>
</div>
<div id="outputs-3" class="section level4">
<h4>Outputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">outputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"std_out"</span>, <span class="dt">label =</span> <span class="st">"std_out"</span>,
<span class="dt">description =</span> <span class="st">"standard output"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>,
<span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">std.out</span><span class="ch">\"</span><span class="st">"</span>),
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"ascat_statistics"</span>, <span class="dt">label =</span> <span class="st">"ascat_statistics"</span>,
<span class="dt">description =</span> <span class="st">"ascat_statistics"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>,
<span class="dt">inheritMetadataFrom =</span> <span class="st">"#normal_bam"</span>, <span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">ascat_output/*.samplestatistics.txt</span><span class="ch">\"</span><span class="st">"</span>)),
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"copynumber_caveman"</span>, <span class="dt">label =</span> <span class="st">"copynumber_caveman"</span>,
<span class="dt">description =</span> <span class="st">"copy_number_caveman"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>,
<span class="dt">inheritMetadataFrom =</span> <span class="st">"#normal_bam"</span>, <span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">ascat_output/*copynumber.caveman.csv</span><span class="ch">\"</span><span class="st">"</span>))
)</code></pre></div>
</div>
</div>
<div id="add-on-scripts" class="section level3 tabset tabset-fade tabset-tabs">
<h3>Add on scripts</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">prep_for_caveman_sh =<span class="st"> </span><span class="kw">fileDef</span>(<span class="dt">name =</span> <span class="st">"prep_for_caveman.sh"</span>, <span class="dt">content =</span> <span class="kw">read_file</span>(<span class="st">"prep_for_caveman.sh"</span>))</code></pre></div>
</div>
<div id="define-tool-object-and-push-to-platform-3" class="section level3 tabset tabset-fade tabset-tabs">
<h3>Define Tool Object and Push to Platform</h3>
<div id="tool-object-3" class="section level4">
<h4>Tool object</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tool <-<span class="st"> </span><span class="kw">Tool</span>(
<span class="dt">id =</span> <span class="st">"ASCAT"</span>,
<span class="dt">label =</span> <span class="st">"ASCAT"</span>,
<span class="dt">hints =</span> <span class="kw">requirements</span>(<span class="kw">docker</span>(<span class="dt">pull =</span> <span class="st">"cgrlab/cgpbox_dev:develop"</span>), <span class="kw">cpu</span>(<span class="dv">1</span>), <span class="kw">mem</span>(<span class="dv">1000</span>)),
<span class="dt">requirements =</span> <span class="kw">requirements</span>(prep_for_caveman_sh),
<span class="dt">baseCommand =</span> <span class="st">"CPU=`grep -c ^processor /proc/cpuinfo` && ascat.pl -c $CPU -rs Human -ra NCBI37 -pr WGS -pl ILLUMINA -sg ascat_SnpGcCorrections.tsv -q 20 -g L -o ascat_output"</span>,
<span class="dt">stdout =</span> <span class="st">"std.out"</span>,
<span class="dt">inputs =</span> inputs,
<span class="dt">arguments =</span> arguments,
<span class="dt">outputs =</span> outputs)</code></pre></div>
</div>
<div id="push-app-to-sbg-platform-3" class="section level4">
<h4>Push app to sbg platform</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">project$<span class="kw">app_add</span>(<span class="st">"ASCAT"</span>, tool)</code></pre></div>
</div>
</div>
</div>
<div id="cgp-pindel" class="section level2 tabset tabset-fade tabset-tabs">
<h2>5. CGP Pindel</h2>
<hr>
<p>Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel</p>
<p><a href="https://github.com/cancerit/cgpPindel" class="uri">https://github.com/cancerit/cgpPindel</a></p>
<div id="base-command-4" class="section level3">
<h3>base command</h3>
<div class="sourceCode"><pre class="sourceCode sh"><code class="sourceCode bash">
<span class="kw">pindel.pl</span>
<span class="kw">-t</span> [tumour mutant bam]
<span class="kw">-n</span> [normal wildtype bam]
<span class="kw">-r</span> [genome reference]
<span class="kw">-c</span> <span class="ot">$CPU</span>
<span class="kw">-sp</span> HUMAN
<span class="kw">-as</span> GRCh37
<span class="kw">-st</span> WGS
<span class="kw">-e</span> NC_007605,hs37d5,GL%
<span class="kw">-s</span> pindel_simpleRepeats.bed.gz
<span class="kw">-f</span> pindel_genomicRules.lst
<span class="kw">-g</span> pindel_human.GRCh37.indelCoding.bed.gz
<span class="kw">-u</span> pindel_pindel_np.gff3.gz
<span class="kw">-sf</span> pindel_softRules.lst
<span class="kw">-b</span> brass-ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz
<span class="kw">-o</span> ./pindel_output</code></pre></div>
<p><br><br><br><br></p>
</div>
<div id="docker-4" class="section level3">
<h3>docker</h3>
<p>The docker conatiner is</p>
<p><code>cgrlab/cgpbox_dev:develop</code></p>
</div>
<div id="app-ports-4" class="section level3 tabset tabset-fade tabset-tabs">
<h3>App ports</h3>
<div id="inputs-4" class="section level4">
<h4>Inputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">inputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"tumour_bam"</span>, <span class="dt">label =</span> <span class="st">"tumour_bam"</span>, <span class="dt">description =</span> <span class="st">"tumour bam"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".bai"</span>), <span class="dt">prefix =</span> <span class="st">"-t"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"normal_bam"</span>, <span class="dt">label =</span> <span class="st">"normal_bam"</span>, <span class="dt">description =</span> <span class="st">"wildtype bam"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".bai"</span>), <span class="dt">prefix =</span> <span class="st">"-n"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"reference"</span>, <span class="dt">label =</span> <span class="st">"reference"</span>, <span class="dt">description =</span> <span class="st">"reference"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".fai"</span>), <span class="dt">prefix =</span> <span class="st">"-r"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"cgpbox_reference_files"</span>, <span class="dt">label =</span> <span class="st">"cgpbox_reference_files"</span>, <span class="dt">description =</span> <span class="st">"extracted reference files"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>, <span class="dt">stageInput =</span> <span class="st">"link"</span>)
)</code></pre></div>
</div>
<div id="arguments-4" class="section level4">
<h4>arguments</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">arguments =<span class="st"> </span><span class="kw">CCBList</span>(<span class="kw">CommandLineBinding</span>(<span class="dt">position =</span> <span class="dv">99</span>, <span class="dt">valueFrom =</span> <span class="kw">list</span>(<span class="st">"</span><span class="ch">\"</span><span class="st">&& ls -lR</span><span class="ch">\"</span><span class="st">"</span>)))</code></pre></div>
</div>
<div id="outputs-4" class="section level4">
<h4>Outputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">outputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"std_out"</span>, <span class="dt">label =</span> <span class="st">"std_out"</span>,
<span class="dt">description =</span> <span class="st">"standard output"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>,
<span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">std.out</span><span class="ch">\"</span><span class="st">"</span>),
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"pindel_germline_bed"</span>, <span class="dt">label =</span> <span class="st">"pindel_germline_bed"</span>,
<span class="dt">description =</span> <span class="st">"pindel_germline_bed output"</span>, <span class="dt">type =</span> <span class="st">"File"</span>,
<span class="dt">inheritMetadataFrom =</span> <span class="st">"#tumour_bam"</span>, <span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">pindel_output/*.germline.bed</span><span class="ch">\"</span><span class="st">"</span>)),
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"pindel_flagged_vcf"</span>, <span class="dt">label =</span> <span class="st">"pindel_flagged_vcf"</span>,
<span class="dt">description =</span> <span class="st">"pindel_flagged_vcf"</span>, <span class="dt">type =</span> <span class="st">"File"</span>,
<span class="dt">inheritMetadataFrom =</span> <span class="st">"#tumour_bam"</span>, <span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">pindel_output/*.flagged.vcf.gz</span><span class="ch">\"</span><span class="st">"</span>), <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".tbi"</span>))
)</code></pre></div>
</div>
</div>
<div id="define-tool-object-and-push-to-platform-4" class="section level3 tabset tabset-fade tabset-tabs">
<h3>Define Tool Object and Push to Platform</h3>
<div id="tool-object-4" class="section level4">
<h4>Tool object</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tool <-<span class="st"> </span><span class="kw">Tool</span>(
<span class="dt">id =</span> <span class="st">"pindel"</span>,
<span class="dt">label =</span> <span class="st">"pindel"</span>,
<span class="dt">hints =</span> <span class="kw">requirements</span>(<span class="kw">docker</span>(<span class="dt">pull =</span> <span class="st">"cgrlab/cgpbox_dev:develop"</span>), <span class="kw">cpu</span>(<span class="dv">1</span>), <span class="kw">mem</span>(<span class="dv">1000</span>)),
<span class="dt">baseCommand =</span> <span class="st">"CPU=`grep -c ^processor /proc/cpuinfo` && pindel.pl -c $CPU -sp HUMAN -as GRCh37 -st WGS -e NC_007605,hs37d5,GL% -s pindel_simpleRepeats.bed.gz -f pindel_genomicRules.lst -g pindel_human.GRCh37.indelCoding.bed.gz -u pindel_pindel_np.gff3.gz -sf pindel_softRules.lst -b brass-ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz -o pindel_output"</span>,
<span class="dt">stdout =</span> <span class="st">"std.out"</span>,
<span class="dt">inputs =</span> inputs,
<span class="dt">arguments =</span> arguments,
<span class="dt">outputs =</span> outputs)</code></pre></div>
</div>
<div id="push-app-to-sbg-platform-4" class="section level4">
<h4>Push app to sbg platform</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">project$<span class="kw">app_add</span>(<span class="st">"pindel"</span>, tool)</code></pre></div>
</div>
</div>
</div>
<div id="caveman" class="section level2 tabset tabset-fade tabset-tabs">
<h2>6. CaVEMan</h2>
<hr>
<p>CaVEMan actually needs the reference index and not the reference (?). But we can attach the reference index as a secondary file to the reference and find the path that way. Need to ask Erik about this.</p>
<p>It uses outputs from Pindel and ASCAT.</p>
<div id="base-command-5" class="section level3">
<h3>base command</h3>
<div class="sourceCode"><pre class="sourceCode sh"><code class="sourceCode bash">
<span class="kw">caveman.pl</span>
<span class="kw">-tb</span> [tumour mutant bam]
<span class="kw">-nb</span> [normal wildtype bam]
<span class="kw">-r</span> [genome reference index - genome.fa.fai]
<span class="kw">-in</span> [pindel .germline.bed]
<span class="kw">-tc</span> [tum.cn.bed - from ASCAT]
<span class="kw">-nc</span> [norm.cn.bed - from ASCAT]
<span class="kw">-t</span> <span class="ot">$CPU</span>
<span class="kw">-s</span> HUMAN
<span class="kw">-sa</span> GRCh37
<span class="kw">-st</span> WGS
<span class="kw">-st</span> genomic
<span class="kw">-ig</span> caveman_ucscHiDepth_0.01_merge1000_no_exon.tsv
<span class="kw">-b</span> ./
<span class="kw">-u</span> ./
<span class="kw">-o</span> caveman_output</code></pre></div>
<p><br><br><br><br></p>
</div>
<div id="docker-5" class="section level3">
<h3>docker</h3>
<p>The docker conatiner is</p>
<p><code>cgrlab/cgpbox_dev:develop</code></p>
</div>
<div id="app-ports-5" class="section level3 tabset tabset-fade tabset-tabs">
<h3>App ports</h3>
<div id="inputs-5" class="section level4">
<h4>Inputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">inputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"tumour_bam"</span>, <span class="dt">label =</span> <span class="st">"tumour_bam"</span>, <span class="dt">description =</span> <span class="st">"mutant tumour bam"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".bai"</span>), <span class="dt">prefix =</span> <span class="st">"-tb"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"normal_bam"</span>, <span class="dt">label =</span> <span class="st">"normal_bam"</span>, <span class="dt">description =</span> <span class="st">"normal wildtype bam"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".bai"</span>), <span class="dt">prefix =</span> <span class="st">"-nb"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"genome_reference"</span>, <span class="dt">label =</span> <span class="st">"genome_reference"</span>, <span class="dt">description =</span> <span class="st">"genome_reference"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".fai"</span>), <span class="dt">valueFrom =</span> <span class="kw">list</span>(<span class="st">"$self.path+</span><span class="ch">\"</span><span class="st">.fai</span><span class="ch">\"</span><span class="st">"</span>), <span class="dt">prefix =</span> <span class="st">"-r"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"pindel_germline_bed"</span>, <span class="dt">label =</span> <span class="st">"pindel_germline_bed"</span>, <span class="dt">description =</span> <span class="st">"pindel_germline_bed"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">prefix =</span> <span class="st">"-in"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"ascat_tumour_cn_bed"</span>, <span class="dt">label =</span> <span class="st">"ascat_tumour_cn_bed"</span>, <span class="dt">description =</span> <span class="st">"ascat_tumour_cn_bed"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">prefix =</span> <span class="st">"-tc"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"ascat_normal_cn_bed"</span>, <span class="dt">label =</span> <span class="st">"ascat_normal_cn_bed"</span>, <span class="dt">description =</span> <span class="st">"ascat_normal_cn_bed"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">prefix =</span> <span class="st">"-nc"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"cgpbox_reference_files"</span>, <span class="dt">label =</span> <span class="st">"cgpbox_reference_files"</span>, <span class="dt">description =</span> <span class="st">"extracted reference files"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>, <span class="dt">stageInput =</span> <span class="st">"link"</span>)
)</code></pre></div>
</div>
<div id="arguments-5" class="section level4">
<h4>arguments</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">arguments =<span class="st"> </span><span class="kw">CCBList</span>(<span class="kw">CommandLineBinding</span>(<span class="dt">position =</span> <span class="dv">99</span>, <span class="dt">valueFrom =</span> <span class="kw">list</span>(<span class="st">"</span><span class="ch">\"</span><span class="st">&& ls -lR</span><span class="ch">\"</span><span class="st">"</span>)))</code></pre></div>
</div>
<div id="outputs-5" class="section level4">
<h4>Outputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">outputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"std_out"</span>, <span class="dt">label =</span> <span class="st">"std_out"</span>,
<span class="dt">description =</span> <span class="st">"standard output"</span>, <span class="dt">type =</span> <span class="st">"File"</span>,
<span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">std.out</span><span class="ch">\"</span><span class="st">"</span>),
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"caveman_snv_bed"</span>, <span class="dt">label =</span> <span class="st">"caveman_snv_bed"</span>,
<span class="dt">description =</span> <span class="st">"caveman_snv_bed"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>,
<span class="dt">inheritMetadataFrom =</span> <span class="st">"#normal_bam"</span>, <span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">caveman_output/*bed</span><span class="ch">\"</span><span class="st">"</span>)),
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"caveman_all_vcf"</span>, <span class="dt">label =</span> <span class="st">"caveman_all_vcf"</span>,
<span class="dt">description =</span> <span class="st">"caveman_all_vcf"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>,
<span class="dt">inheritMetadataFrom =</span> <span class="st">"#normal_bam"</span>, <span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">caveman_output/*vcf.gz</span><span class="ch">\"</span><span class="st">"</span>), <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".tbi"</span>)),
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"caveman_flagged_muts_vcf"</span>, <span class="dt">label =</span> <span class="st">"caveman_flagged_muts_vcf"</span>,
<span class="dt">description =</span> <span class="st">"caveman_flagged_muts_vcf"</span>, <span class="dt">type =</span> <span class="st">"File"</span>,
<span class="dt">inheritMetadataFrom =</span> <span class="st">"#normal_bam"</span>, <span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span><span class="st">"</span><span class="ch">\"</span><span class="st">caveman_output/*flagged.muts.vcf.gz</span><span class="ch">\"</span><span class="st">"</span>), <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".tbi"</span>))
)</code></pre></div>
</div>
</div>
<div id="define-tool-object-and-push-to-platform-5" class="section level3 tabset tabset-fade tabset-tabs">
<h3>Define Tool Object and Push to Platform</h3>
<div id="tool-object-5" class="section level4">
<h4>Tool object</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tool <-<span class="st"> </span><span class="kw">Tool</span>(
<span class="dt">id =</span> <span class="st">"CaVEMan"</span>,
<span class="dt">label =</span> <span class="st">"CaVEMan"</span>,
<span class="dt">hints =</span> <span class="kw">requirements</span>(<span class="kw">docker</span>(<span class="dt">pull =</span> <span class="st">"cgrlab/cgpbox_dev:develop"</span>), <span class="kw">mem</span>(<span class="dv">1000</span>)),
<span class="dt">baseCommand =</span> <span class="st">"CPU=`grep -c ^processor /proc/cpuinfo` && caveman.pl -t $CPU -s HUMAN -sa GRCh37 -st WGS -st genomic -ig caveman_ucscHiDepth_0.01_merge1000_no_exon.tsv -b ./ -u ./ -o caveman_output"</span>,
<span class="dt">stdout =</span> <span class="st">"std.out"</span>,
<span class="dt">inputs =</span> inputs,
<span class="dt">arguments =</span> arguments,
<span class="dt">outputs =</span> outputs)</code></pre></div>
</div>
<div id="push-app-to-sbg-platform-5" class="section level4">
<h4>Push app to sbg platform</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">project$<span class="kw">app_add</span>(<span class="st">"CaVEMan"</span>, tool)</code></pre></div>
</div>
</div>
<div id="notes" class="section level3">
<h3>notes</h3>
<p>needs these 3 inputs from other tools</p>
<pre><code>-in /datastore/output/${NAME_MT}_vs_${NAME_WT}/pindel/${NAME_MT}_vs_${NAME_WT}.germline.bed \
-tc $TMP/tum.cn.bed \
-nc $TMP/norm.cn.bed \</code></pre>
<p>Prep ASCAT for caveman</p>
<pre><code>echo -e "CaVEMan prep: `date`"
set -x
ASCAT_CN="/datastore/output/${NAME_MT}_vs_${NAME_WT}/ascat/$NAME_MT.copynumber.caveman.csv"
perl -ne '@F=(split q{,}, $_)[1,2,3,4]; $F[1]-1; print join("\t",@F)."\n";' < $ASCAT_CN > $TMP/norm.cn.bed
perl -ne '@F=(split q{,}, $_)[1,2,3,6]; $F[1]-1; print join("\t",@F)."\n";' < $ASCAT_CN > $TMP/tum.cn.bed
set +x
</code></pre>
</div>
</div>
<div id="brass" class="section level2 tabset tabset-fade tabset-tabs">
<h2>7. Brass</h2>
<hr>
<p>Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements.</p>
<p><a href="https://github.com/cancerit/BRASS" class="uri">https://github.com/cancerit/BRASS</a></p>
<div id="base-command-6" class="section level3">
<h3>base command</h3>
<div class="sourceCode"><pre class="sourceCode sh"><code class="sourceCode bash">
<span class="kw">brass.pl</span>
<span class="kw">-t</span> [tumour bam]
<span class="kw">-n</span> [normal wildtype bam]
<span class="kw">-g</span> [genome reference]
<span class="kw">-ss</span> [ascat *.samplestatistics.txt array]
<span class="kw">-j</span> 4
<span class="kw">-k</span> 4
<span class="kw">-c</span> <span class="ot">$CPU</span>
<span class="kw">-s</span> HUMAN
<span class="kw">-as</span> GRCh37
<span class="kw">-pr</span> WGS
<span class="kw">-pl</span> ILLUMINA
<span class="kw">-d</span> brass-ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz
<span class="kw">-f</span> brass-brass_np.groups.gz
<span class="kw">-g_cache</span> vagrent_Homo_sapiens.GRCh37.75.vagrent.cache.gz
<span class="kw">-vi</span> brass-viral.1.1.genomic.fa
<span class="kw">-mi</span> brass-all_ncbi_bacteria.20150703
<span class="kw">-b</span> brass-hs37d5_500bp_windows.gc.bed.gz
<span class="kw">-ct</span> brass-Human.GRCh37.CentTelo.tsv
<span class="kw">-o</span> ./brass_output</code></pre></div>
<p><br><br><br><br></p>
</div>
<div id="docker-6" class="section level3">
<h3>docker</h3>
<p>The docker conatiner is</p>
<p><code>cgrlab/cgpbox_dev:develop</code></p>
</div>
<div id="app-ports-6" class="section level3 tabset tabset-fade tabset-tabs">
<h3>App ports</h3>
<div id="inputs-6" class="section level4">
<h4>Inputs</h4>
<p>Need to add more inputs here.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">inputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"tumour_bam"</span>, <span class="dt">label =</span> <span class="st">"tumour_bam"</span>, <span class="dt">description =</span> <span class="st">"tumour bam"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">stageInput =</span> <span class="st">"link"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".bai"</span>), <span class="dt">valueFrom =</span> <span class="kw">list</span>(<span class="st">"{return $self.name}"</span>), <span class="dt">prefix =</span> <span class="st">"-t"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"normal_bam"</span>, <span class="dt">label =</span> <span class="st">"normal_bam"</span>, <span class="dt">description =</span> <span class="st">"wildtype bam"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">stageInput =</span> <span class="st">"link"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".bai"</span>), <span class="dt">valueFrom =</span> <span class="kw">list</span>(<span class="st">"{return $self.name}"</span>), <span class="dt">prefix =</span> <span class="st">"-n"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"genome_reference"</span>, <span class="dt">label =</span> <span class="st">"genome_reference"</span>, <span class="dt">description =</span> <span class="st">"genome_reference"</span>, <span class="dt">type =</span> <span class="st">"File"</span>, <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".fai"</span>), <span class="dt">prefix =</span> <span class="st">"-g"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"bam_stats"</span>, <span class="dt">label =</span> <span class="st">"bam_stats"</span>, <span class="dt">description =</span> <span class="st">"bam stats"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>, <span class="dt">stageInput =</span> <span class="st">"link"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"ascat_sample_statistics"</span>, <span class="dt">label =</span> <span class="st">"ascat_sample_statistics"</span>, <span class="dt">description =</span> <span class="st">"ascat_sample_statistics"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>, <span class="dt">prefix =</span> <span class="st">"-ss"</span>),
<span class="kw">input</span>(<span class="dt">id =</span> <span class="st">"cgpbox_reference_files"</span>, <span class="dt">label =</span> <span class="st">"cgpbox_reference_files"</span>, <span class="dt">description =</span> <span class="st">"extracted reference files"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>, <span class="dt">stageInput =</span> <span class="st">"link"</span>)
)</code></pre></div>
</div>
<div id="arguments-6" class="section level4">
<h4>arguments</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">arguments =<span class="st"> </span><span class="kw">CCBList</span>(<span class="kw">CommandLineBinding</span>(<span class="dt">position =</span> <span class="dv">99</span>, <span class="dt">valueFrom =</span> <span class="kw">list</span>(<span class="st">"</span><span class="ch">\"</span><span class="st">&& ls -lR</span><span class="ch">\"</span><span class="st">"</span>)))</code></pre></div>
</div>
<div id="outputs-6" class="section level4">
<h4>Outputs</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">outputs =<span class="st"> </span><span class="kw">list</span>(
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"std_out"</span>, <span class="dt">label =</span> <span class="st">"std_out"</span>,
<span class="dt">description =</span> <span class="st">"standard output"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>,
<span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">std.out</span><span class="ch">\"</span><span class="st">"</span>),
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"brass_sv_bedpe"</span>, <span class="dt">label =</span> <span class="st">"brass_sv_bedpe"</span>,
<span class="dt">description =</span> <span class="st">"brass_sv_bedpe"</span>, <span class="dt">type =</span> <span class="st">"File"</span>,
<span class="dt">inheritMetadataFrom =</span> <span class="st">"#normal_bam"</span>, <span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">brass_output/*bedpe.gz</span><span class="ch">\"</span><span class="st">"</span>), <span class="dt">secondaryFiles =</span> <span class="kw">list</span>(<span class="st">".tbi"</span>)),
<span class="kw">output</span>(<span class="dt">id =</span> <span class="st">"brass_vcf"</span>, <span class="dt">label =</span> <span class="st">"brass_vcf"</span>,
<span class="dt">description =</span> <span class="st">"brass_vcf"</span>, <span class="dt">type =</span> <span class="st">"File..."</span>,
<span class="dt">inheritMetadataFrom =</span> <span class="st">"#normal_bam"</span>, <span class="dt">metadata =</span> <span class="kw">list</span>(<span class="dt">org =</span> <span class="st">"cgp"</span>),
<span class="dt">glob =</span> <span class="kw">Expression</span>(<span class="dt">engine =</span> <span class="st">"#cwl-js-engine"</span>,
<span class="dt">script =</span> <span class="st">"</span><span class="ch">\"</span><span class="st">brass_output/*vcf*</span><span class="ch">\"</span><span class="st">"</span>))
)</code></pre></div>
</div>
</div>
<div id="define-tool-object-and-push-to-platform-6" class="section level3 tabset tabset-fade tabset-tabs">
<h3>Define Tool Object and Push to Platform</h3>
<div id="tool-object-6" class="section level4">
<h4>Tool object</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">tool <-<span class="st"> </span><span class="kw">Tool</span>(
<span class="dt">id =</span> <span class="st">"BRASS"</span>,
<span class="dt">label =</span> <span class="st">"BRASS"</span>,
<span class="dt">hints =</span> <span class="kw">requirements</span>(<span class="kw">docker</span>(<span class="dt">pull =</span> <span class="st">"cgrlab/cgpbox_dev:develop"</span>), <span class="kw">cpu</span>(<span class="dv">1</span>), <span class="kw">mem</span>(<span class="dv">1000</span>)),
<span class="dt">baseCommand =</span> <span class="st">"CPU=`grep -c ^processor /proc/cpuinfo` && brass.pl -j 4 -k 4 -c $CPU -s HUMAN -as GRCh37 -pr WGS -pl ILLUMINA -d brass-ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz -f brass-brass_np.groups.gz -g_cache vagrent_Homo_sapiens.GRCh37.75.vagrent.cache.gz -vi brass-viral.1.1.genomic.fa -mi brass-all_ncbi_bacteria.20150703 -b brass-hs37d5_500bp_windows.gc.bed.gz -ct brass-Human.GRCh37.CentTelo.tsv -o ./brass_output"</span>,
<span class="dt">stdout =</span> <span class="st">"std.out"</span>, <span class="dt">inputs =</span> inputs, <span class="dt">arguments =</span> arguments, <span class="dt">outputs =</span> outputs)</code></pre></div>
</div>