chipseq/modules/local/frip_score.nf at 779ce9a2b4ff97b2024c091d403d81baec118642 · nf-core/chipseq · GitHub

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process FRIP_SCORE {
    tag "$meta.id"
    label 'process_medium'

    conda "bioconda::bedtools=2.30.0 bioconda::samtools=1.15.1"
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:3127fcae6b6bdaf8181e21a26ae61231030a9fcb-0':
        'biocontainers/mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:3127fcae6b6bdaf8181e21a26ae61231030a9fcb-0' }"

    input:
    tuple val(meta), path(bam), path(peak)

    output:
    tuple val(meta), path("*.txt"), emit: txt
    path "versions.yml"           , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    def args   = task.ext.args   ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    """
    READS_IN_PEAKS=\$(intersectBed -a $bam -b $peak $args | awk -F '\t' '{sum += \$NF} END {print sum}')
    samtools flagstat $bam > ${bam}.flagstat
    grep 'mapped (' ${bam}.flagstat | grep -v "primary" | awk -v a="\$READS_IN_PEAKS" -v OFS='\t' '{print "${prefix}", a/\$1}' > ${prefix}.FRiP.txt

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    END_VERSIONS
    """

    stub:
    def prefix = task.ext.prefix ?: "${meta.id}"
    """
    touch ${prefix}.FRiP.txt

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    END_VERSIONS
    """
}