process BBMAP_ALIGN { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' : 'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' }" input: tuple val(meta), path(fastq) path ref output: tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.log"), emit: log path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}" // Set the db variable to reflect the three possible types of reference input: 1) directory // named 'ref', 2) directory named something else (containg a 'ref' subdir) or 3) a sequence // file in fasta format if ( ref.isDirectory() ) { if ( ref ==~ /(.\/)?ref\/?/ ) { db = '' } else { db = "path=${ref}" } } else { db = "ref=${ref}" } """ bbmap.sh \\ $db \\ $input \\ out=${prefix}.bam \\ $args \\ threads=$task.cpus \\ -Xmx${task.memory.toGiga()}g \\ &> ${prefix}.bbmap.log cat <<-END_VERSIONS > versions.yml "${task.process}": bbmap: \$(bbversion.sh) samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) END_VERSIONS """ }