id: 'nf-core-methylseq-summary'
description: ' - this information is collected when the pipeline is started.'
section_name: 'nf-core/methylseq Workflow Summary'
section_href: 'https://github.com/nf-core/methylseq'
plot_type: 'html'
data: |
    <p style="font-size:110%"><b>Input/output options</b></p>
    <dl class="dl-horizontal">
        <dt>input</dt><dd><samp>/gscratch/scrubbed/strigg/analyses/20250829_meth_Apul/samplesheet.csv</samp></dd>
        <dt>outdir</dt><dd><samp>/gscratch/scrubbed/strigg/analyses/20250829_meth_Apul</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/Apulcra-genome.fa</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Special library types</b></p>
    <dl class="dl-horizontal">
        <dt>em_seq</dt><dd><samp>true</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Bismark options</b></p>
    <dl class="dl-horizontal">
        <dt>nomeseq</dt><dd><samp>true</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Skip pipeline steps</b></p>
    <dl class="dl-horizontal">
        <dt>skip_trimming</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>2025-08-29_10-21-02</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Core Nextflow options</b></p>
    <dl class="dl-horizontal">
        <dt>configFiles</dt><dd><samp>/mmfs1/gscratch/srlab/nextflow/bin/assets/nf-core/methylseq/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/20250829_meth_Apul</samp></dd>
        <dt>profile</dt><dd><samp>standard</samp></dd>
        <dt>projectDir</dt><dd><samp>/mmfs1/gscratch/srlab/nextflow/bin/assets/nf-core/methylseq</samp></dd>
        <dt>revision</dt><dd><samp>master</samp></dd>
        <dt>runName</dt><dd><samp>voluminous_meitner</samp></dd>
        <dt>userName</dt><dd><samp>strigg</samp></dd>
        <dt>workDir</dt><dd><samp>/mmfs1/gscratch/scrubbed/strigg/analyses/20250829_meth_Apul/work</samp></dd>
    </dl>