process SAMBLASTER { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.14" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0' : 'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0' }" input: tuple val(meta), path(bam) output: tuple val(meta), path("*.bam"), emit: bam path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def args3 = task.ext.args3 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" if( "$bam" == "${prefix}.bam" ) error "Input and output names are the same, use the suffix option to disambiguate" """ samtools view -h $args2 $bam | \\ samblaster $args | \\ samtools view $args3 -Sb - >${prefix}.bam cat <<-END_VERSIONS > versions.yml "${task.process}": samblaster: \$( samblaster -h 2>&1 | head -n 1 | sed 's/^samblaster: Version //' ) samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ }