process BBMAP_BBSPLIT { label 'process_high' conda (params.enable_conda ? "bioconda::bbmap=38.93" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.93--he522d1c_0' : 'quay.io/biocontainers/bbmap:38.93--he522d1c_0' }" input: tuple val(meta), path(reads) path index path primary_ref tuple val(other_ref_names), path (other_ref_paths) val only_build_index output: path "bbsplit" , optional:true, emit: index tuple val(meta), path('*primary*fastq.gz'), optional:true, emit: primary_fastq tuple val(meta), path('*fastq.gz') , optional:true, emit: all_fastq tuple val(meta), path('*txt') , optional:true, emit: stats path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3 if (!task.memory) { log.info '[BBSplit] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } def other_refs = [] other_ref_names.eachWithIndex { name, index -> other_refs << "ref_${name}=${other_ref_paths[index]}" } if (only_build_index) { if (primary_ref && other_ref_names && other_ref_paths) { """ bbsplit.sh \\ -Xmx${avail_mem}g \\ ref_primary=$primary_ref \\ ${other_refs.join(' ')} \\ path=bbsplit \\ threads=$task.cpus \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": bbmap: \$(bbversion.sh 2>&1) END_VERSIONS """ } else { log.error 'ERROR: Please specify as input a primary fasta file along with names and paths to non-primary fasta files.' } } else { def index_files = '' if (index) { index_files = "path=$index" } else if (primary_ref && other_ref_names && other_ref_paths) { index_files = "ref_primary=${primary_ref} ${other_refs.join(' ')}" } else { log.error 'ERROR: Please either specify a BBSplit index as input or a primary fasta file along with names and paths to non-primary fasta files.' } def fastq_in = meta.single_end ? "in=${reads}" : "in=${reads[0]} in2=${reads[1]}" def fastq_out = meta.single_end ? "basename=${prefix}_%.fastq.gz" : "basename=${prefix}_%_#.fastq.gz" """ bbsplit.sh \\ -Xmx${avail_mem}g \\ $index_files \\ threads=$task.cpus \\ $fastq_in \\ $fastq_out \\ refstats=${prefix}.stats.txt \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": bbmap: \$(bbversion.sh 2>&1) END_VERSIONS """ } }