process SAMTOOLS_FIXMATE { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.14" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" input: tuple val(meta), path(bam) output: tuple val(meta), path("*.bam"), emit: bam path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ samtools \\ fixmate \\ $args \\ --threads ${task.cpus-1} \\ $bam \\ ${prefix}.bam \\ cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ }