id: 'nf-core-rnaseq-summary'
description: ' - this information is collected when the pipeline is started.'
section_name: 'nf-core/rnaseq Workflow Summary'
section_href: 'https://github.com/nf-core/rnaseq'
plot_type: 'html'
data: |
    <p style="font-size:110%"><b>Core Nextflow options</b></p>
    <dl class="dl-horizontal">
        <dt>runName</dt><dd><samp>voluminous_visvesvaraya</samp></dd>
        <dt>containerEngine</dt><dd><samp>singularity</samp></dd>
        <dt>launchDir</dt><dd><samp>/gscratch/scrubbed/samwhite/outputs/20220323-pgen-nextflow_rnaseq-tissues</samp></dd>
        <dt>workDir</dt><dd><samp>/gscratch/scrubbed/samwhite/outputs/20220323-pgen-nextflow_rnaseq-tissues/work</samp></dd>
        <dt>projectDir</dt><dd><samp>/gscratch/srlab/programs/nf-core-rnaseq-3.6/workflow</samp></dd>
        <dt>userName</dt><dd><samp>samwhite</samp></dd>
        <dt>profile</dt><dd><samp>singularity</samp></dd>
        <dt>configFiles</dt><dd><samp>/gscratch/srlab/programs/nf-core-rnaseq-3.6/workflow/nextflow.config, /gscratch/srlab/programs/nf-core-rnaseq-3.6/configs/conf/base-srlab_500GB_node.config</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Input/output options</b></p>
    <dl class="dl-horizontal">
        <dt>input</dt><dd><samp>sample_sheet-2666621.csv</samp></dd>
        <dt>outdir</dt><dd><samp>/gscratch/scrubbed/samwhite/outputs/20220323-pgen-nextflow_rnaseq-tissues</samp></dd>
        <dt>multiqc_title</dt><dd><samp>20220321-pgen-nextflow_rnaseq-tissues-2666621</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/sam/data/P_generosa/genomes/Panopea-generosa-v1.0.fa</samp></dd>
        <dt>gff</dt><dd><samp>/gscratch/srlab/sam/data/P_generosa/genomes/Panopea-generosa-v1.0.a4_biotype-trna_strand_converted-no_RNAmmer.gff</samp></dd>
        <dt>save_reference</dt><dd><samp>true</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Read trimming options</b></p>
    <dl class="dl-horizontal">
        <dt>trim_nextseq</dt><dd><samp>20</samp></dd>
        <dt>save_trimmed</dt><dd><samp>true</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Alignment options</b></p>
    <dl class="dl-horizontal">
        <dt>pseudo_aligner</dt><dd><samp>salmon</samp></dd>
        <dt>save_align_intermeds</dt><dd><samp>true</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Institutional config options</b></p>
    <dl class="dl-horizontal">
        <dt>custom_config_base</dt><dd><samp>/gscratch/srlab/programs/nf-core-rnaseq-3.6/workflow/../configs/</samp></dd>
    </dl>