process SAMTOOLS_BAM2FQ { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(inputbam) val split output: tuple val(meta), path("*.fq.gz"), emit: reads 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}" if (split){ """ samtools \\ bam2fq \\ $args \\ -@ $task.cpus \\ -1 ${prefix}_1.fq.gz \\ -2 ${prefix}_2.fq.gz \\ -0 ${prefix}_other.fq.gz \\ -s ${prefix}_singleton.fq.gz \\ $inputbam cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ } else { """ samtools \\ bam2fq \\ $args \\ -@ $task.cpus \\ $inputbam >${prefix}_interleaved.fq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ } }