id: 'nf-core-chipseq-summary'
description: ' - this information is collected when the pipeline is started.'
section_name: 'nf-core/chipseq Workflow Summary'
section_href: 'https://github.com/nf-core/chipseq'
plot_type: 'html'
data: |
    <p style="font-size:110%"><b>Core Nextflow options</b></p>
    <dl class="dl-horizontal">
        <dt>revision</dt><dd><samp>master</samp></dd>
        <dt>runName</dt><dd><samp>reverent_joliot</samp></dd>
        <dt>containerEngine</dt><dd><samp>docker</samp></dd>
        <dt>launchDir</dt><dd><samp>/var/www-iscsi-data-1/www/lifesci/pub/penguin/~vcalvanese/viviensu</samp></dd>
        <dt>workDir</dt><dd><samp>/var/www-iscsi-data-1/www/lifesci/pub/penguin/~vcalvanese/viviensu/work</samp></dd>
        <dt>projectDir</dt><dd><samp>/home/mikkolalab/.nextflow/assets/nf-core/chipseq</samp></dd>
        <dt>userName</dt><dd><samp>mikkolalab</samp></dd>
        <dt>profile</dt><dd><samp>docker</samp></dd>
        <dt>configFiles</dt><dd><samp><span style="color:#999999;">N/A</a></samp></dd>
    </dl>
    <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>read_length</dt><dd><samp>100</samp></dd>
        <dt>outdir</dt><dd><samp>results_chipseq</samp></dd>
    </dl>
    <p style="font-size:110%"><b>Reference genome options</b></p>
    <dl class="dl-horizontal">
        <dt>genome</dt><dd><samp>hg19</samp></dd>
        <dt>fasta</dt><dd><samp>s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa</samp></dd>
        <dt>gtf</dt><dd><samp>s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf</samp></dd>
        <dt>bwa_index</dt><dd><samp>s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/</samp></dd>
        <dt>bowtie2_index</dt><dd><samp>s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/</samp></dd>
        <dt>star_index</dt><dd><samp>s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/STARIndex/</samp></dd>
        <dt>macs_gsize</dt><dd><samp>2700000000</samp></dd>
        <dt>blacklist</dt><dd><samp>/home/mikkolalab/.nextflow/assets/nf-core/chipseq/assets/blacklists/v1.0/hg19-blacklist.v1.bed</samp></dd>
    </dl>