process SAMTOOLS_MERGE { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" input: tuple val(meta), path(input_files, stageAs: "?/*") path fasta path fai output: tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram tuple val(meta), path("*.csi") , optional:true, emit: csi path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension() def reference = fasta ? "--reference ${fasta}" : "" """ samtools \\ merge \\ --threads ${task.cpus-1} \\ $args \\ ${reference} \\ ${prefix}.${file_type} \\ $input_files cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ stub: prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension() """ touch ${prefix}.${file_type} cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ }