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<span>Input Arguments</span>
</h2>
</doc-anchor-target>
<p>Each of the main Harpy modules (e.g. <code v-pre>qc</code> or <code v-pre>phase</code>) follows the format of</p>
<p>Each of the main Harpy modules (e.g. <a href="../modules/qc/" class="no-link inline-flex align-middle items-center justify-center font-medium leading-none whitespace-nowrap text-blue-600 bg-blue-100 border border-blue-100 hover:border-blue-300 dark:hover:bg-blue-200 transition-colors duration-200 ease-out h-6 px-2 text-xs rounded-full">
<span>qc</span>
</a> or <a href="../modules/phase/" class="no-link inline-flex align-middle items-center justify-center font-medium leading-none whitespace-nowrap text-blue-600 bg-blue-100 border border-blue-100 hover:border-blue-300 dark:hover:bg-blue-200 transition-colors duration-200 ease-out h-6 px-2 text-xs rounded-full">
<span>phase</span>
</a>) follows the format of</p>
<div class="codeblock-wrapper"><doc-codeblock>
<pre class="language-bash"><code v-pre class="language-bash">harpy module options arguments</code></pre>
</doc-codeblock></div>
<p>where <code v-pre>module</code> is something like <code v-pre>impute</code> or <code v-pre>snp mpileup</code> and <code v-pre>options</code> are the runtime parameters,
<p>where <code v-pre>module</code> is something like <a href="../modules/impute/" class="no-link inline-flex align-middle items-center justify-center font-medium leading-none whitespace-nowrap text-blue-600 bg-blue-100 border border-blue-100 hover:border-blue-300 dark:hover:bg-blue-200 transition-colors duration-200 ease-out h-6 px-2 text-xs rounded-full">
<span>impute</span>
</a> or <a href="../modules/snp/" class="no-link inline-flex align-middle items-center justify-center font-medium leading-none whitespace-nowrap text-blue-600 bg-blue-100 border border-blue-100 hover:border-blue-300 dark:hover:bg-blue-200 transition-colors duration-200 ease-out h-6 px-2 text-xs rounded-full">
<span>snp mpileup</span>
</a> and <code v-pre>options</code> are the runtime parameters,
which can include things like an input <code v-pre>--vcf</code> file, <code v-pre>--molecule-distance</code>, etc. After the options
is where you provide the input files/directories without flags and following standard BASH expansion
rules (e.g. wildcards). You can mix and match entire directories, individual files, and wildcard expansions.
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</doc-anchor-target>
<p>Every Harpy module has a series of configuration parameters. These are arguments you need to input
to configure the module to run on your data, such as the directory with the reads/alignments,
the genome assembly, etc. All main modules (e.g. <code v-pre>qc</code>) also share a series of common runtime
the genome assembly, etc. All main modules (e.g. <a href="../modules/qc/" class="no-link inline-flex align-middle items-center justify-center font-medium leading-none whitespace-nowrap text-blue-600 bg-blue-100 border border-blue-100 hover:border-blue-300 dark:hover:bg-blue-200 transition-colors duration-200 ease-out h-6 px-2 text-xs rounded-full">
<span>qc</span>
</a>) also share a series of common runtime
parameters that don&#x27;t impact the results of the module, but instead control the speed/verbosity/etc.
of calling the module. These runtime parameters are listed in the modules&#x27; help strings and can be
configured using these arguments:</p>
<div class="table-wrapper scrollbar overflow-hidden">
<table class="comfortable">
<table class="compact">
<thead>
<tr>
<th style="text-align: left;">argument</th>
<th style="text-align: center;">short name</th>
<th style="text-align: left;">type</th>
<th style="text-align: center;">default</th>
<th style="text-align: center;">required</th>
<th style="text-align: left;">description</th>
</tr>
</thead>
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<td style="text-align: center;"><code v-pre>-o</code></td>
<td style="text-align: left;">string</td>
<td style="text-align: center;">varies</td>
<td style="text-align: center;">no</td>
<td style="text-align: left;">Name of output directory</td>
</tr>
<tr>
<td style="text-align: left;"><code v-pre>--threads</code></td>
<td style="text-align: center;"><code v-pre>-t</code></td>
<td style="text-align: left;">integer</td>
<td style="text-align: center;">4</td>
<td style="text-align: center;">no</td>
<td style="text-align: left;">Number of threads to use</td>
</tr>
<tr>
<td style="text-align: left;"><code v-pre>--conda</code></td>
<td style="text-align: center;"></td>
<td style="text-align: left;">toggle</td>
<td style="text-align: center;"></td>
<td style="text-align: left;">Use local conda environments instead of preconfigured Singularity container</td>
</tr>
<tr>
<td style="text-align: left;"><code v-pre>--skipreports</code></td>
<td style="text-align: center;"><code v-pre>-r</code></td>
<td style="text-align: center;"></td>
<td style="text-align: left;">toggle</td>
<td style="text-align: center;"></td>
<td style="text-align: center;">no</td>
<td style="text-align: left;">Skip the processing and generation of HTML reports in a workflow</td>
</tr>
<tr>
<td style="text-align: left;"><code v-pre>--snakemake</code></td>
<td style="text-align: center;"><code v-pre>-s</code></td>
<td style="text-align: center;"></td>
<td style="text-align: left;">string</td>
<td style="text-align: center;"></td>
<td style="text-align: center;">no</td>
<td style="text-align: left;">Additional <a href="../snakemake/#adding-snakamake-parameters">Snakemake</a> options, in quotes</td>
</tr>
<tr>
<td style="text-align: left;"><code v-pre>--quiet</code></td>
<td style="text-align: center;"><code v-pre>-q</code></td>
<td style="text-align: left;">toggle</td>
<td style="text-align: center;"></td>
<td style="text-align: center;">no</td>
<td style="text-align: left;">Supressing Snakemake printing to console</td>
<td style="text-align: left;">Suppress Snakemake printing to console</td>
</tr>
<tr>
<td style="text-align: left;"><code v-pre>--help</code></td>
<td style="text-align: center;"></td>
<td style="text-align: center;"><code v-pre>-h</code></td>
<td style="text-align: left;"></td>
<td style="text-align: center;"></td>
<td style="text-align: center;"></td>
<td style="text-align: left;">Show the module docstring</td>
</tr>
</tbody>
</table>
</div>
<p>As as example, you could call the <code v-pre>harpy align</code> module and specify 20 threads with no output to console:</p>
<p>As as example, you could call <a href="../modules/align/minimap/" class="no-link inline-flex align-middle items-center justify-center font-medium leading-none whitespace-nowrap text-blue-600 bg-blue-100 border border-blue-100 hover:border-blue-300 dark:hover:bg-blue-200 transition-colors duration-200 ease-out h-6 px-2 text-xs rounded-full">
<span>align minimap</span>
</a> and specify 20 threads with no output to console:</p>
<div class="codeblock-wrapper"><doc-codeblock>
<pre class="language-bash"><code v-pre class="language-bash">harpy align bwa --threads 20 --quiet samples/trimmedreads
<pre class="language-bash"><code v-pre class="language-bash">harpy align minimap --threads 20 --quiet samples/trimmedreads

# identical to #

harpy align bwa -t 20 -q samples/trimmedreads</code></pre>
harpy align minimap -t 20 -q samples/trimmedreads</code></pre>
</doc-codeblock></div>
<hr>
<doc-anchor-target id="the-workflow-folder">
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understanding or as a point of reference when writing the Methods within a manuscript. The presence of the folder
and the contents therein also allow you to rerun the workflow manually. The <code v-pre>workflow</code> folder may contain the following:</p>
<div class="table-wrapper scrollbar overflow-hidden">
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<table class="compact">
<thead>
<tr>
<th style="text-align: left;">item</th>
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<td style="text-align: left;">useful to understand math behind plots/tables or borrow code from</td>
</tr>
<tr>
<td style="text-align: left;"><code v-pre>*.workflow.summary</code></td>
<td style="text-align: left;"><code v-pre>*.summary</code></td>
<td style="text-align: left;">Plain-text overview of the important parts of the workflow</td>
<td style="text-align: left;">useful for bookkeeping and writing Methods</td>
</tr>
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</doc-anchor-target>
<p>You will notice that many of the workflows will create a <code v-pre>Genome</code> folder in the working
directory. This folder is to make it easier for Harpy to store the genome and the associated
indexing/etc. files. Your input genome will be symlinked into that directory (not copied), but
all the other files (<code v-pre>.fai</code>, <code v-pre>.bwt</code>, <code v-pre>.bed</code>, etc.) will be created in that directory.</p>
indexing/etc. files across workflows without having to redo things unnecessarily. Your input
genome will be symlinked into that directory (not copied, unless a workflow requires gzipping/decompressing),
but all the other files (<code v-pre>.fai</code>, <code v-pre>.bwt</code>, <code v-pre>.bed</code>, etc.) will be created in that directory.</p>


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