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<!DOCTYPE html>
<html lang="en">
<head>
<link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Overpass:300,400,600,800">
<script src="https://code.jquery.com/jquery-3.4.1.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<meta charset="utf-8"/>
<title>V-pipe configuration</title>
</head>
<body onload="anchorOnLoad();" id="root"><div class="text-right">
<button class="btn btn-primary" type="button" data-toggle="collapse" data-target=".collapse:not(.show)" aria-expanded="false">Expand all</button>
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</div>
<div class="breadcrumbs"></div> <h1>V-pipe configuration</h1><span class="badge badge-dark value-type">Type: object</span><br/>
<span class="description"><p>The V-pipe workflow can be customized through the configuration file <code>config.yaml</code> or <code>config.json</code> or, for backward compatibility with the <a href="https://github.com/cbg-ethz/V-pipe/wiki/options">legacy INI-style format used in V-pipe v1.x/2.x</a>, <code>vpipe.config</code>. This configuration file is a text file written using a basic structure composed of sections, properties and values. When using <a href="https://yaml.org/spec/1.0/#id2564813">YAML</a> or <a href="https://www.json.org/json-en.html">JSON</a> format use these languages associative array/dictionaries in two levels for sections and properties. When using the older <a href="https://docs.python.org/3/library/configparser.html">INI format</a>, sections are expected in squared brackets, and properties are followed by corresponding values.</p>
<p>Further more, it is possible to specify additional options on the command line using Snakemake’s <code>--configfile</code> to pass additional YAML/JSON configuration files, and/or using Snakemake’s <code>--config</code> to pass sections and properties in a <a href="https://yaml.org/spec/1.2.0/#Flow">YAML Flow style</a>/JSON syntax.</p>
<p>The order of precedence is:<br />
<em>command line options (<code>--config</code>, <code>--configfile</code>)</em> >> <em>default configuration file (<code>config/config.yaml</code> or <code>config.yaml</code>)</em> >> <em>legacy configuration INI (<code>vpipe.config</code>)</em> >> <em>Virus-specific base config (<code>virus_based_config</code>)</em> >> <em>default values</em></p>
<p>Example: For instance, we suggest providing as input a tabular file specifying sample unique identifiers (e.g., patient identifiers), and dates for different sequencing runs related to the same patient. The name of this file (here, <code>samples.tsv</code>) can be provided by specifying the section as <code>input</code> and the property as <code>samples_file</code>, as follows in the example below.</p>
<p>In this document, we provide a comprehensive list of all user-configurable options stratified by sections.</p>
</span>
<br/>
<div class="badge badge-secondary">Example:</div>
<br/><div id="root_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="nt">input</span><span class="p">:</span>
<span class="w"> </span><span class="nt">samples_file</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">samples.tsv</span>
</pre></div>
</div>
<div class="accordion" id="accordiongeneral">
<div class="card">
<div class="card-header" id="headinggeneral">
<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#general"
aria-expanded="" aria-controls="general" onclick="setAnchor('#general')"><span class="property-name">general</span></button>
</h2>
</div>
<div id="general"
class="collapse property-definition-div" aria-labelledby="headinggeneral"
data-parent="#accordiongeneral">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general" onclick="anchorLink('general')">general</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br/>
<span class="description"><p>This section of the configuration provides general options that control the overall behavior of the pipeline.</p>
</span>
<div class="accordion" id="accordiongeneral_virus_base_config">
<div class="card">
<div class="card-header" id="headinggeneral_virus_base_config">
<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#general_virus_base_config"
aria-expanded="" aria-controls="general_virus_base_config" onclick="setAnchor('#general_virus_base_config')"><span class="property-name">virus_base_config</span></button>
</h2>
</div>
<div id="general_virus_base_config"
class="collapse property-definition-div" aria-labelledby="headinggeneral_virus_base_config"
data-parent="#accordiongeneral_virus_base_config">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general" onclick="anchorLink('general')">general</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general_virus_base_config" onclick="anchorLink('general_virus_base_config')">virus_base_config</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br/>
<span class="description"><p>We provide virus-specific base configuration files which contain handy defaults for, e.g., HIV and SARS-CoV-2. Check the git repository’s <a href="https://github.com/cbg-ethz/V-pipe/tree/master/config#virus_base_config">config subdirectory</a> to learn about them.</p>
</span>
<br/>
<div class="badge badge-secondary">Examples:</div>
<br/><div id="general_virus_base_config_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">hiv</span>
</pre></div>
</div><div id="general_virus_base_config_ex2" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">sars-cov-2</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="accordiongeneral_preprocessor">
<div class="card">
<div class="card-header" id="headinggeneral_preprocessor">
<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#general_preprocessor"
aria-expanded="" aria-controls="general_preprocessor" onclick="setAnchor('#general_preprocessor')"><span class="property-name">preprocessor</span></button>
</h2>
</div>
<div id="general_preprocessor"
class="collapse property-definition-div" aria-labelledby="headinggeneral_preprocessor"
data-parent="#accordiongeneral_preprocessor">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general" onclick="anchorLink('general')">general</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general_preprocessor" onclick="anchorLink('general_preprocessor')">preprocessor</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "prinseq"</span><br/>
<span class="description"><p>By default trimming and clipping of reads is performed by PRINSEQ <sup class="footnote-ref" id="fnref-10"><a href="#fn-10">1</a></sup> – a versatile raw read processor for short-reads with many customization options, that we use mostly for Illumina short-read sequencing.<br />
Some other sequencing platforms, e.g., Oxford Nanopore Technologies, are not compatible with this software and usually perform quality control during the fast5 basecalling and demultiplexing anyway, e.g., by Guppy. Use <code>skip</code> to avoid performing preprocessing such already quality-trimmed fastq files.</p>
<div class="footnotes">
<hr />
<ol>
<li id="fn-10">
<p>Schmieder, R. and Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011. <a href="#fnref-10" class="footnoteBackLink" title="Jump back to footnote 1 in the text.">↩</a></p>
</li>
</ol>
</div>
</span><div class="enum-value" id="general_preprocessor_enum">
<h4>Must be one of:</h4>
<ul class="list-group"><li class="list-group-item enum-item">"prinseq"</li><li class="list-group-item enum-item">"skip"</li><li class="list-group-item enum-item">""</li></ul>
</div>
<br/>
<div class="badge badge-secondary">Example:</div>
<br/><div id="general_preprocessor_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">skip</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="accordiongeneral_aligner">
<div class="card">
<div class="card-header" id="headinggeneral_aligner">
<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#general_aligner"
aria-expanded="" aria-controls="general_aligner" onclick="setAnchor('#general_aligner')"><span class="property-name">aligner</span></button>
</h2>
</div>
<div id="general_aligner"
class="collapse property-definition-div" aria-labelledby="headinggeneral_aligner"
data-parent="#accordiongeneral_aligner">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general" onclick="anchorLink('general')">general</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general_aligner" onclick="anchorLink('general_aligner')">aligner</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "ngshmmalign"</span><br/>
<span class="description"><p>There are three options for mapping reads, either using <a href="https://github.com/cbg-ethz/ngshmmalign"><code>ngshmmalign</code></a>, <a href="https://github.com/lh3/bwa">BWA MEM (<code>bwa</code>)</a> <sup class="footnote-ref" id="fnref-1"><a href="#fn-1">1</a></sup>, <a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml">Bowtie 2 (<code>bowtie</code>)</a> <sup class="footnote-ref" id="fnref-2"><a href="#fn-2">2</a></sup>, or <a href="https://lh3.github.io/minimap2/">minimap2 (<code>minimap</code>)</a><sup class="footnote-ref" id="fnref-11"><a href="#fn-11">3</a></sup>. To use a different aligner than the default, indicate which aligner you want to use by setting the property aligner.</p>
<p><strong>Note</strong>: Some virus-specific base configuration specified in <code>virus_base_config</code> might change this option’s default to a more appropriate aligner for that virus, e.g., depending on its usual diversity and mutation rate.<br />
You are still free to override that default in your configuration shall the need arise.</p>
<div class="footnotes">
<hr />
<ol>
<li id="fn-1">
<p>Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013. <a href="#fnref-1" class="footnoteBackLink" title="Jump back to footnote 1 in the text.">↩</a></p>
</li>
<li id="fn-2">
<p>Langmead, B. and Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012. <a href="#fnref-2" class="footnoteBackLink" title="Jump back to footnote 2 in the text.">↩</a></p>
</li>
<li id="fn-11">
<p>Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018. <a href="#fnref-11" class="footnoteBackLink" title="Jump back to footnote 3 in the text.">↩</a></p>
</li>
</ol>
</div>
</span><div class="enum-value" id="general_aligner_enum">
<h4>Must be one of:</h4>
<ul class="list-group"><li class="list-group-item enum-item">"ngshmmalign"</li><li class="list-group-item enum-item">"bwa"</li><li class="list-group-item enum-item">"bowtie"</li><li class="list-group-item enum-item">"minimap"</li></ul>
</div>
<br/>
<div class="badge badge-secondary">Example:</div>
<br/><div id="general_aligner_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">minimap</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="accordiongeneral_primers_trimmer">
<div class="card">
<div class="card-header" id="headinggeneral_primers_trimmer">
<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#general_primers_trimmer"
aria-expanded="" aria-controls="general_primers_trimmer" onclick="setAnchor('#general_primers_trimmer')"><span class="property-name">primers_trimmer</span></button>
</h2>
</div>
<div id="general_primers_trimmer"
class="collapse property-definition-div" aria-labelledby="headinggeneral_primers_trimmer"
data-parent="#accordiongeneral_primers_trimmer">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general" onclick="anchorLink('general')">general</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general_primers_trimmer" onclick="anchorLink('general_primers_trimmer')">primers_trimmer</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "ivar"</span><br/>
<span class="description"><p>There are two options available for trimming primers, either using <a href="https://andersen-lab.github.io/ivar/html/">iVar trim (<code>ivar</code>)</a> <sup class="footnote-ref" id="fnref-3"><a href="#fn-3">1</a></sup> or <a href="http://www.htslib.org/doc/samtools-ampliconclip.html">Samtools ampliconclip (<code>samtools</code>)</a> <sup class="footnote-ref" id="fnref-4"><a href="#fn-4">2</a></sup>. iVar trim is used by default. If you prefer to use Samtools ampliconclip, then indicate so in the configuration file as in the example</p>
<div class="footnotes">
<hr />
<ol>
<li id="fn-3">
<p>Grubaugh, N. et al. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biology. 2019. <a href="#fnref-3" class="footnoteBackLink" title="Jump back to footnote 1 in the text.">↩</a></p>
</li>
<li id="fn-4">
<p>Danecek P, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021 <a href="#fnref-4" class="footnoteBackLink" title="Jump back to footnote 2 in the text.">↩</a></p>
</li>
</ol>
</div>
</span><div class="enum-value" id="general_primers_trimmer_enum">
<h4>Must be one of:</h4>
<ul class="list-group"><li class="list-group-item enum-item">"ivar"</li><li class="list-group-item enum-item">"samtools"</li></ul>
</div>
<br/>
<div class="badge badge-secondary">Example:</div>
<br/><div id="general_primers_trimmer_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">samtools</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="accordiongeneral_snv_caller">
<div class="card">
<div class="card-header" id="headinggeneral_snv_caller">
<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#general_snv_caller"
aria-expanded="" aria-controls="general_snv_caller" onclick="setAnchor('#general_snv_caller')"><span class="property-name">snv_caller</span></button>
</h2>
</div>
<div id="general_snv_caller"
class="collapse property-definition-div" aria-labelledby="headinggeneral_snv_caller"
data-parent="#accordiongeneral_snv_caller">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general" onclick="anchorLink('general')">general</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general_snv_caller" onclick="anchorLink('general_snv_caller')">snv_caller</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "shorah"</span><br/>
<span class="description"><p>There are three options available for calling single nucleotide variants, either using <a href="https://github.com/cbg-ethz/shorah">ShoRAH (<code>shorah</code>)</a> <sup class="footnote-ref" id="fnref-5"><a href="#fn-5">1</a></sup>, <a href="https://csb5.github.io/lofreq/">LoFreq (<code>lofreq</code>)</a> <sup class="footnote-ref" id="fnref-6"><a href="#fn-6">2</a></sup> or <a href="https://github.com/cbg-ethz/viloca">VILOCA (<code>viloca</code>)</a> [^7] . ShoRAH is used by default. If you prefer to use LoFreq, then indicate so in the configuration file as in the example</p>
<div class="footnotes">
<hr />
<ol>
<li id="fn-5">
<p>Zagordi, O. et al. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics. 2011. <a href="#fnref-5" class="footnoteBackLink" title="Jump back to footnote 1 in the text.">↩</a></p>
</li>
<li id="fn-6">
<p>Wilm, A. et al. LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012. <a href="#fnref-6" class="footnoteBackLink" title="Jump back to footnote 2 in the text.">↩</a></p>
</li>
</ol>
</div>
</span><div class="enum-value" id="general_snv_caller_enum">
<h4>Must be one of:</h4>
<ul class="list-group"><li class="list-group-item enum-item">"shorah"</li><li class="list-group-item enum-item">"lofreq"</li><li class="list-group-item enum-item">"viloca"</li></ul>
</div>
<br/>
<div class="badge badge-secondary">Example:</div>
<br/><div id="general_snv_caller_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">lofreq</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="accordiongeneral_haplotype_reconstruction">
<div class="card">
<div class="card-header" id="headinggeneral_haplotype_reconstruction">
<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#general_haplotype_reconstruction"
aria-expanded="" aria-controls="general_haplotype_reconstruction" onclick="setAnchor('#general_haplotype_reconstruction')"><span class="property-name">haplotype_reconstruction</span></button>
</h2>
</div>
<div id="general_haplotype_reconstruction"
class="collapse property-definition-div" aria-labelledby="headinggeneral_haplotype_reconstruction"
data-parent="#accordiongeneral_haplotype_reconstruction">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general" onclick="anchorLink('general')">general</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general_haplotype_reconstruction" onclick="anchorLink('general_haplotype_reconstruction')">haplotype_reconstruction</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "savage"</span><br/>
<span class="description"><p>There are three options available for haplotype reconstruction, namely <a href="https://github.com/HaploConduct/HaploConduct/tree/master/savage">SAVAGE</a> <sup class="footnote-ref" id="fnref-7"><a href="#fn-7">1</a></sup>, <a href="https://github.com/cbg-ethz/haploclique">HaploClique</a> <sup class="footnote-ref" id="fnref-8"><a href="#fn-8">2</a></sup> or <a href="https://github.com/cbg-ethz/predicthaplo/">PredictHaplo</a> <sup class="footnote-ref" id="fnref-9"><a href="#fn-9">3</a></sup>. SAVAGE is used by default. If you wish to use HaploClique, then indicate it in the configuration file as in the example.</p>
<div class="footnotes">
<hr />
<ol>
<li id="fn-7">
<p>Baaijens, J. A. et al., De novo assembly of viral quasispecies using overlap graphs. Genome Res. 2017. <a href="#fnref-7" class="footnoteBackLink" title="Jump back to footnote 1 in the text.">↩</a></p>
</li>
<li id="fn-8">
<p>Töpfer, A. et al. Viral quasispecies assembly via maximal clique finding. PLOS Computational Biology. 2014. <a href="#fnref-8" class="footnoteBackLink" title="Jump back to footnote 2 in the text.">↩</a></p>
</li>
<li id="fn-9">
<p>Prabhakaran, S. et al. HIV haplotype inference using a propagating dirichlet process mixture model. IEEE/ACM transactions on computational biology and bioinformatics 11.1. 2013. <a href="#fnref-9" class="footnoteBackLink" title="Jump back to footnote 3 in the text.">↩</a></p>
</li>
</ol>
</div>
</span><div class="enum-value" id="general_haplotype_reconstruction_enum">
<h4>Must be one of:</h4>
<ul class="list-group"><li class="list-group-item enum-item">"savage"</li><li class="list-group-item enum-item">"haploclique"</li><li class="list-group-item enum-item">"predicthaplo"</li></ul>
</div>
<br/>
<div class="badge badge-secondary">Example:</div>
<br/><div id="general_haplotype_reconstruction_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">haploclique</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="accordiongeneral_threads">
<div class="card">
<div class="card-header" id="headinggeneral_threads">
<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#general_threads"
aria-expanded="" aria-controls="general_threads" onclick="setAnchor('#general_threads')"><span class="property-name">threads</span></button>
</h2>
</div>
<div id="general_threads"
class="collapse property-definition-div" aria-labelledby="headinggeneral_threads"
data-parent="#accordiongeneral_threads">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general" onclick="anchorLink('general')">general</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general_threads" onclick="anchorLink('general_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1</span><br/>
<span class="description"><p>This option should be used to specify the default number of threads for all multi-threaded rules. That is, unless the number of threads is specified for each rule, this value is set as default.</p>
</span>
<p><span class="badge badge-light restriction numeric-restriction" id="general_threads_number">Value must be greater or equal to <code>1</code></span></p>
<br/>
<div class="badge badge-secondary">Example:</div>
<br/><div id="general_threads_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">4</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="accordiongeneral_checksum">
<div class="card">
<div class="card-header" id="headinggeneral_checksum">
<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#general_checksum"
aria-expanded="" aria-controls="general_checksum" onclick="setAnchor('#general_checksum')"><span class="property-name">checksum</span></button>
</h2>
</div>
<div id="general_checksum"
class="collapse property-definition-div" aria-labelledby="headinggeneral_checksum"
data-parent="#accordiongeneral_checksum">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general" onclick="anchorLink('general')">general</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general_checksum" onclick="anchorLink('general_checksum')">checksum</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "md5"</span><br/>
<span class="description"><p>Sets the algorithm to be used when computing checksums for uploadable data.</p>
</span><div class="enum-value" id="general_checksum_enum">
<h4>Must be one of:</h4>
<ul class="list-group"><li class="list-group-item enum-item">"md5"</li><li class="list-group-item enum-item">"sha1"</li><li class="list-group-item enum-item">"sha256"</li><li class="list-group-item enum-item">"sha224"</li><li class="list-group-item enum-item">"sha384"</li><li class="list-group-item enum-item">"sha512"</li><li class="list-group-item enum-item">"xxh64"</li><li class="list-group-item enum-item">"xxh32"</li><li class="list-group-item enum-item">"xxh128"</li></ul>
</div>
<br/>
<div class="badge badge-secondary">Example:</div>
<br/><div id="general_checksum_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">sha256</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="accordiongeneral_temp_prefix">
<div class="card">
<div class="card-header" id="headinggeneral_temp_prefix">
<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#general_temp_prefix"
aria-expanded="" aria-controls="general_temp_prefix" onclick="setAnchor('#general_temp_prefix')"><span class="property-name">temp_prefix</span></button>
</h2>
</div>
<div id="general_temp_prefix"
class="collapse property-definition-div" aria-labelledby="headinggeneral_temp_prefix"
data-parent="#accordiongeneral_temp_prefix">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general" onclick="anchorLink('general')">general</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general_temp_prefix" onclick="anchorLink('general_temp_prefix')">temp_prefix</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br/>
<span class="description"><p>Some step of V-pipe produce temporary files such as, e.g., decompressed intermediate — i.e. files which aren’t kept long-term but are deleted after all steps that needed them have finished. By default, these files are written in the output data directory. This option, makes it is possible to write them in a different directory instead. Use this option to, e.g., leverage a faster cluster-local storage or avoid wasting backup space on a snapshotted storage. You might want to consult the documentation provided by your HPC.</p>
</span>
<br/>
<div class="badge badge-secondary">Examples:</div>
<br/><div id="general_temp_prefix_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">temp</span>
</pre></div>
</div><div id="general_temp_prefix_ex2" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">/cluster/scratch</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="accordiongeneral_tsvbased">
<div class="card">
<div class="card-header" id="headinggeneral_tsvbased">
<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#general_tsvbased"
aria-expanded="" aria-controls="general_tsvbased" onclick="setAnchor('#general_tsvbased')"><span class="property-name">tsvbased</span></button>
</h2>
</div>
<div id="general_tsvbased"
class="collapse property-definition-div" aria-labelledby="headinggeneral_tsvbased"
data-parent="#accordiongeneral_tsvbased">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general" onclick="anchorLink('general')">general</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general_tsvbased" onclick="anchorLink('general_tsvbased')">tsvbased</a></div><span class="badge badge-dark value-type">Type: enum (of integer)</span> <span class="badge badge-success default-value">Default: 1</span><br/>
<span class="description"><p>Specify whether TSV files like coverage and base counts should be 1-based (i.e.: the first base pair position is called <code>1</code>) like standard practice used in biology and most text formats such as VCF and GFF, or should be 0-based (i.e.: the first base pair position is called <code>0</code>) like in several Python tools such as pysam and the BED format.</p>
<p>By default V-pipe uses 1-based TSV file (position column starts with <code>1</code>), but this option change the behaviour.</p>
</span><div class="enum-value" id="general_tsvbased_enum">
<h4>Must be one of:</h4>
<ul class="list-group"><li class="list-group-item enum-item">0</li><li class="list-group-item enum-item">1</li></ul>
</div>
<br/>
<div class="badge badge-secondary">Example:</div>
<br/><div id="general_tsvbased_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">0</span>
</pre></div>
</div>
</div>
</div>
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<div class="accordion" id="accordiongeneral_id_separator">
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<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#general_id_separator"
aria-expanded="" aria-controls="general_id_separator" onclick="setAnchor('#general_id_separator')"><span class="property-name">id_separator</span></button>
</h2>
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class="collapse property-definition-div" aria-labelledby="headinggeneral_id_separator"
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fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
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fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#general_id_separator" onclick="anchorLink('general_id_separator')">id_separator</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "/"</span><br/>
<span class="description"><p>Charater to use when assembling the two levels (e.g.: sample and a date), into a column title to be used in a report TSV file</p>
<p>E.g., with this sample file</p>
<pre><code>patient1 20100113
patient1 20110202
patient2 20081130
</code></pre>
<p>the coverage TSV file’s column will be called <code>patient1/20100113</code>, <code>patient1/20110202</code> and <code>patient2/20081130</code>.</p>
</span>
<br/>
<div class="badge badge-secondary">Example:</div>
<br/><div id="general_id_separator_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="p p-Indicator">-</span>
</pre></div>
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<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#input"
aria-expanded="" aria-controls="input" onclick="setAnchor('#input')"><span class="property-name">input</span></button>
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class="collapse property-definition-div" aria-labelledby="headinginput"
data-parent="#accordioninput">
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<div class="breadcrumbs">root
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d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#input" onclick="anchorLink('input')">input</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br/>
<span class="description"><p>Properties in this section of the configuration control the input of the pipeline.</p>
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<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#input" onclick="anchorLink('input')">input</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#input_datadir" onclick="anchorLink('input_datadir')">datadir</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "samples/"</span><br/>
<span class="description"><p>The input file for the workflow will be searched in this directory.</p>
<p>V-pipe expects the input samples to be organized in a two-level directory hierarchy.</p>
<ul>
<li>The first level can be, e.g., patient samples or biological replicates of an experiment.</li>
<li>The second level can be, e.g., different sampling dates or different sequencing runs of the same sample.</li>
<li>Inside that directory, the sub-directory <code>raw_data</code> holds the sequencing data in FASTQ format (optionally compressed with GZip).</li>
</ul>
<p>For example:</p>
<div class="highlight jumbotron">
<pre><span></span><code>📁samples
├──📁patient1
│ ├──📁20100113
│ │ └──📁raw_data
│ │ ├──🧬patient1_20100113_R1.fastq
│ │ └──🧬patient1_20100113_R2.fastq
│ └──📁20110202
│ └──📁raw_data
│ ├──🧬patient1_20100202_R1.fastq
│ └──🧬patient1_20100202_R2.fastq
└──📁patient2
└──📁20081130
└──📁raw_data
├──🧬patient2_20081130_R1.fastq.gz
└──🧬patient2_20081130_R2.fastq.gz
</code></pre>
</div>
</span>
<br/>
<div class="badge badge-secondary">Examples:</div>
<br/><div id="input_datadir_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">tests/data/hiv/</span>
</pre></div>
</div><div id="input_datadir_ex2" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">tests/data/sars-cov-2/</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
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aria-expanded="" aria-controls="input_paired" onclick="setAnchor('#input_paired')"><span class="property-name">paired</span></button>
</h2>
</div>
<div id="input_paired"
class="collapse property-definition-div" aria-labelledby="headinginput_paired"
data-parent="#accordioninput_paired">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#input" onclick="anchorLink('input')">input</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#input_paired" onclick="anchorLink('input_paired')">paired</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: true</span><br/>
<span class="description"><p>Indicate whether the input sequencing reads correspond to paired-end reads.</p>
<p>Paired-ended reads need to be in split files with <code>_R1</code> and <code>_R2</code> suffixes:</p>
<div class="highlight jumbotron">
<pre><span></span><code>📁raw_data
├──🧬patient2_20081130_R1.fastq.gz
└──🧬patient2_20081130_R2.fastq.gz
</code></pre>
</div>
</span>
<br/>
<div class="badge badge-secondary">Example:</div>
<br/><div id="input_paired_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">False</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="accordioninput_fastq_suffix">
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<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#input_fastq_suffix"
aria-expanded="" aria-controls="input_fastq_suffix" onclick="setAnchor('#input_fastq_suffix')"><span class="property-name">fastq_suffix</span></button>
</h2>
</div>
<div id="input_fastq_suffix"
class="collapse property-definition-div" aria-labelledby="headinginput_fastq_suffix"
data-parent="#accordioninput_fastq_suffix">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#input" onclick="anchorLink('input')">input</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#input_fastq_suffix" onclick="anchorLink('input_fastq_suffix')">fastq_suffix</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br/>
<span class="description"><p>V-pipe expects paired-end reads to be in files that end in <code>_R1</code> and <code>_R2</code> exactly right before the file extension, e.g., <code>_R1.fastq.gz</code>, because this is how the workflow finds and recognizes them.</p>
<p>But Illumina’s bcl2fastq demultiplexer might introduce additional strings, e.g., <code>_R2_001.fast.gz</code> or, depending on its <em>mismatches</em> settings, e.g., <code>_R2_001_MM_1.fast.gz</code>. Use this options to specify anything which should go between the <code>_R1</code> and <code>_R2</code> endings and the file extension.</p>
</span>
<br/>
<div class="badge badge-secondary">Examples:</div>
<br/><div id="input_fastq_suffix_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">_001</span>
</pre></div>
</div><div id="input_fastq_suffix_ex2" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">_001_MM_1</span>
</pre></div>
</div>
</div>
</div>
</div>
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aria-expanded="" aria-controls="input_samples_file" onclick="setAnchor('#input_samples_file')"><span class="property-name">samples_file</span></button>
</h2>
</div>
<div id="input_samples_file"
class="collapse property-definition-div" aria-labelledby="headinginput_samples_file"
data-parent="#accordioninput_samples_file">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#input" onclick="anchorLink('input')">input</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#input_samples_file" onclick="anchorLink('input_samples_file')">samples_file</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "config/samples.tsv"</span><br/>
<span class="description"><p>File containing sample unique identifiers and dates as tab-separated values, e.g.,</p>
<pre><code>patient1 20100113
patient1 20110202
patient2 20081130
</code></pre>
<p>Here, we have two samples from patient 1 and one sample from patient 2. By default, V-pipe searches for a file named samples.tsv, if this file does not exist, a list of samples is built by globbing datadir directory contents.</p>
<p>Optionally, the samples file can contain a third column specifying the read length. This is particularly useful when samples are sequenced using protocols with different read lengths.</p>
<p>Optionally, a fourth column can contain a short name of a protocol (e.g.: <code>v3</code>) that is detailed in the file specified in <a href="#input_protocols_file"><code>input</code> => <code>protocols_file</code></a>. This is useful if protocol details such as primers change over time, e.g. to adapt to new variants with SNV breaking primer binding affinity.</p>
<p>Standardized Snakemake workflows place their tables inside the <code>config/</code> subdirectory, but using this options you can specify alternate locations, e.g., the current working directory (as done in legacy V-pipe v1.x/2.x).</p>
</span>
<br/>
<div class="badge badge-secondary">Example:</div>
<br/><div id="input_samples_file_ex1" class="jumbotron examples"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">samples.tsv</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="accordioninput_protocols_file">
<div class="card">
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<h2 class="mb-0">
<button class="btn btn-link property-name-button" type="button" data-toggle="collapse" data-target="#input_protocols_file"
aria-expanded="" aria-controls="input_protocols_file" onclick="setAnchor('#input_protocols_file')"><span class="property-name">protocols_file</span></button>
</h2>
</div>
<div id="input_protocols_file"
class="collapse property-definition-div" aria-labelledby="headinginput_protocols_file"
data-parent="#accordioninput_protocols_file">
<div class="card-body pl-5">
<div class="breadcrumbs">root
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#input" onclick="anchorLink('input')">input</a>
<svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-arrow-right-short" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
<path
fill-rule="evenodd"
d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"
/>
</svg>
<a href="#input_protocols_file" onclick="anchorLink('input_protocols_file')">protocols_file</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br/>
<span class="description"><p>When different samples have been processed with different library protocols, this file specifies a lookup table with per-protocol specific (primers bed and fasta), eg.:</p>
<div class="highlight jumbotron">
<pre><span></span><code><span class="nt">v41</span><span class="p">:</span>
<span class="w"> </span><span class="nt">name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">SARS-CoV-2 ARTIC V4.1</span>
<span class="w"> </span><span class="nt">inserts_bedfile</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v41/SARS-CoV-2.insert.bed</span>
<span class="w"> </span><span class="nt">primers_bedfile</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v41/SARS-CoV-2.primer.bed</span>
<span class="w"> </span><span class="nt">primers_file</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v41/SARS-CoV-2.tsv</span>
<span class="w"> </span><span class="nt">primers_fasta</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v41/SARS-CoV-2.primer.fasta</span>
<span class="nt">v4</span><span class="p">:</span>
<span class="w"> </span><span class="nt">name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">SARS-CoV-2 ARTIC V4</span>
<span class="w"> </span><span class="nt">inserts_bedfile</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v4/SARS-CoV-2.insert.bed</span>
<span class="w"> </span><span class="nt">primers_bedfile</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v4/SARS-CoV-2.primer.bed</span>
<span class="w"> </span><span class="nt">primers_file</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v4/SARS-CoV-2.tsv</span>
<span class="w"> </span><span class="nt">primers_fasta</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v4/ARTIC_v4.fasta</span>
<span class="nt">v3</span><span class="p">:</span>
<span class="w"> </span><span class="nt">name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">SARS-CoV-2 ARTIC V3</span>
<span class="w"> </span><span class="nt">inserts_bedfile</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v3/nCoV-2019.insert.bed</span>
<span class="w"> </span><span class="nt">primers_bedfile</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v3/nCoV-2019.primer.bed</span>
<span class="w"> </span><span class="nt">primers_file</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v3/nCoV-2019.tsv</span>
<span class="w"> </span><span class="nt">primers_fasta</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v3/ARTIC_v3.fasta</span>