process BBMAP_BBDUK { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.90" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1' : 'quay.io/biocontainers/bbmap:38.90--he522d1c_1' }" input: tuple val(meta), path(reads) path contaminants output: tuple val(meta), path('*.fastq.gz'), emit: reads 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 ?: "${meta.id}" def raw = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}" def trimmed = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz" def contaminants_fa = contaminants ? "ref=$contaminants" : '' """ maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g') bbduk.sh \\ -Xmx\$maxmem \\ $raw \\ $trimmed \\ threads=$task.cpus \\ $args \\ $contaminants_fa \\ &> ${prefix}.bbduk.log cat <<-END_VERSIONS > versions.yml "${task.process}": bbmap: \$(bbversion.sh) END_VERSIONS """ }