bam_remove_orphans.nf

/*
 * Remove orphan reads from paired-end BAM file
 */
process BAM_REMOVE_ORPHANS {
    tag "$meta.id"
    label 'process_medium'

    conda "bioconda::pysam=0.19.0 bioconda::samtools=1.15.1"
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/mulled-v2-57736af1eb98c01010848572c9fec9fff6ffaafd:402e865b8f6af2f3e58c6fc8d57127ff0144b2c7-0' :
        'biocontainers/mulled-v2-57736af1eb98c01010848572c9fec9fff6ffaafd:402e865b8f6af2f3e58c6fc8d57127ff0144b2c7-0' }"

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

    output:
    tuple val(meta), path("${prefix}.bam"), emit: bam
    path "versions.yml"                   , emit: versions

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

    script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/
    def args = task.ext.args ?: ''
    prefix   = task.ext.prefix ?: "${meta.id}"
    if (!meta.single_end) {
        """
        samtools sort -n -@ $task.cpus -o ${prefix}.name.sorted.bam -T ${prefix}.name.sorted $bam
        bampe_rm_orphan.py ${prefix}.name.sorted.bam ${prefix}.bam $args

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

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

    stub:
    prefix = task.ext.prefix ?: "${meta.id}"
    """
    touch ${prefix}.bam

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