id: 'nf-core-rnavar-summary'
description: ' - this information is collected when the pipeline is started.'
section_name: 'nf-core/rnavar Workflow Summary'
section_href: 'https://github.com/nf-core/rnavar'
plot_type: 'html'
data: |
    <p style="font-size:110%"><b>Input/output options</b></p>
    <dl class="dl-horizontal">
        <dt>input</dt><dd><samp>samplesheet.csv</samp></dd>
        <dt>outdir</dt><dd><samp>result</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Reference genome options</b></p>
    <dl class="dl-horizontal">
        <dt>fasta</dt><dd><samp>/gscratch/srlab/strigg/GENOMES/Pocillopora_meandrina_HIv1.assembly.fasta</samp></dd>
        <dt>genome</dt><dd><samp>null</samp></dd>
        <dt>gtf</dt><dd><samp>/gscratch/srlab/strigg/GENOMES/Pocillopora_meandrina_HIv1.genes-validated.gtf</samp></dd>
        <dt>igenomes_ignore</dt><dd><samp>true</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Alignment options</b></p>
    <dl class="dl-horizontal">
        <dt>star_twopass</dt><dd><samp>true</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Pipeline stage options</b></p>
    <dl class="dl-horizontal">
        <dt>skip_baserecalibration</dt><dd><samp>true</samp></dd>
        <dt>skip_variantannotation</dt><dd><samp>true</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Institutional config options</b></p>
    <dl class="dl-horizontal">
        <dt>config_profile_contact</dt><dd><samp>Shelly A. Wanamaker @shellywanamaker</samp></dd>
        <dt>config_profile_description</dt><dd><samp>UW Hyak Roberts labs cluster profile provided by nf-core/configs.</samp></dd>
        <dt>config_profile_url</dt><dd><samp>https://faculty.washington.edu/sr320/</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Generic options</b></p>
    <dl class="dl-horizontal">
        <dt>trace_report_suffix</dt><dd><samp>2025-07-21_19-17-29</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Core Nextflow options</b></p>
    <dl class="dl-horizontal">
        <dt>configFiles</dt><dd><samp>/mmfs1/home/strigg/.nextflow/assets/nf-core/rnavar/nextflow.config, /gscratch/srlab/strigg/bin/uw_hyak_srlab.config</samp></dd>
        <dt>containerEngine</dt><dd><samp>singularity</samp></dd>
        <dt>launchDir</dt><dd><samp>/mmfs1/gscratch/scrubbed/strigg/analyses/20250721_rnavar</samp></dd>
        <dt>profile</dt><dd><samp>standard</samp></dd>
        <dt>projectDir</dt><dd><samp>/mmfs1/home/strigg/.nextflow/assets/nf-core/rnavar</samp></dd>
        <dt>revision</dt><dd><samp>master</samp></dd>
        <dt>runName</dt><dd><samp>sick_murdock</samp></dd>
        <dt>userName</dt><dd><samp>strigg</samp></dd>
        <dt>workDir</dt><dd><samp>/mmfs1/gscratch/scrubbed/strigg/analyses/20250721_rnavar/work</samp></dd>
    </dl>