process IVAR_TRIM { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : 'quay.io/biocontainers/ivar:1.3.1--h089eab3_0' }" input: tuple val(meta), path(bam), path(bai) path bed output: tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path('*.log'), emit: log path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" """ ivar trim \\ $args \\ -i $bam \\ -b $bed \\ -p $prefix \\ > ${prefix}.ivar.log cat <<-END_VERSIONS > versions.yml "${task.process}": ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//') END_VERSIONS """ }