process BWAMEM2_MEM { tag "$meta.id" label 'process_high' conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' : 'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' }" input: tuple val(meta), path(reads) path index val sort_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 args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def read_group = meta.read_group ? "-R ${meta.read_group}" : "" def samtools_command = sort_bam ? 'sort' : 'view' """ INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'` bwa-mem2 \\ mem \\ $args \\ $read_group \\ -t $task.cpus \\ \$INDEX \\ $reads \\ | samtools $samtools_command $args2 -@ $task.cpus -o ${prefix}.bam - cat <<-END_VERSIONS > versions.yml "${task.process}": bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bam cat <<-END_VERSIONS > versions.yml "${task.process}": bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ }