id: 'sarek-summary'
description: " - this information is collected when the pipeline is started."
section_name: 'nf-core/sarek Workflow Summary'
section_href: 'https://github.com/nf-core/sarek'
plot_type: 'html'
data: |
    <dl class="dl-horizontal">
        <dt>Pipeline Release</dt><dd><samp>master</samp></dd>
        <dt>Run Name</dt><dd><samp>clever_euler</samp></dd>
        <dt>Max Resources</dt><dd><samp>120 GB memory, 10 cpus, 4d time per job</samp></dd>
        <dt>Container</dt><dd><samp>singularity - nfcore/sarek:2.7.1</samp></dd>
        <dt>Output dir</dt><dd><samp>./results</samp></dd>
        <dt>Launch dir</dt><dd><samp>/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples</samp></dd>
        <dt>Working dir</dt><dd><samp>/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work</samp></dd>
        <dt>Script dir</dt><dd><samp>/home/sigenae/.nextflow/assets/nf-core/sarek</samp></dd>
        <dt>User</dt><dd><samp>sigenae</samp></dd>
        <dt>Input</dt><dd><samp>/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/input.tsv</samp></dd>
        <dt>Step</dt><dd><samp>mapping</samp></dd>
        <dt>Genome</dt><dd><samp>Gallus_gallus-5.0</samp></dd>
        <dt>Nucleotides/s</dt><dd><samp>1000</samp></dd>
        <dt>Tools</dt><dd><samp>haplotypecaller, freebayes, mpileup</samp></dd>
        <dt>MarkDuplicates</dt><dd><samp>Options</samp></dd>
        <dt>Java options</dt><dd><samp>"-Xms4000m -Xmx7g"</samp></dd>
        <dt>GATK Spark</dt><dd><samp>No</samp></dd>
        <dt>Save BAMs mapped</dt><dd><samp>No</samp></dd>
        <dt>Skip MarkDuplicates</dt><dd><samp>No</samp></dd>
        <dt>GVCF</dt><dd><samp>Yes</samp></dd>
        <dt>AWS iGenomes base</dt><dd><samp>s3://ngi-igenomes/igenomes/</samp></dd>
        <dt>Genomes base</dt><dd><samp>/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data/</samp></dd>
        <dt>Save Reference</dt><dd><samp>No</samp></dd>
        <dt>BWA indexes</dt><dd><samp>/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa.{amb,ann,bwt,pac,sa}</samp></dd>
        <dt>dict</dt><dd><samp>/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.dict</samp></dd>
        <dt>fasta reference</dt><dd><samp>/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa</samp></dd>
        <dt>known indels</dt><dd><samp>/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus_incl_consequences.vcf</samp></dd>
        <dt>known indels index</dt><dd><samp>/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus_incl_consequences.vcf.idx</samp></dd>
        <dt>Publish dir mode</dt><dd><samp>copy</samp></dd>
        <dt>Config Profile</dt><dd><samp>standard</samp></dd>
        <dt>Config Description</dt><dd><samp>The Genotoul cluster profile</samp></dd>
        <dt>Config Contact</dt><dd><samp>support.bioinfo.genotoul@inra.fr</samp></dd>
        <dt>Config URL</dt><dd><samp>http://bioinfo.genotoul.fr/</samp></dd>
        <dt>Config Files</dt><dd><samp>/home/sigenae/.nextflow/assets/nf-core/sarek/nextflow.config, /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/./genotoul_1.config</samp></dd>
    </dl>