process BWA_SAMPE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' : 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }" input: tuple val(meta), path(reads), path(sai) path index 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}" def read_group = meta.read_group ? "-r ${meta.read_group}" : "" """ INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'` bwa sampe \\ $args \\ $read_group \\ \$INDEX \\ $sai \\ $reads | samtools sort -@ ${task.cpus - 1} -O bam - > ${prefix}.bam cat <<-END_VERSIONS > versions.yml "${task.process}": bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ }