process TRIMGALORE { tag "$meta.id" label 'process_high' conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : 'quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0' }" input: tuple val(meta), path(reads) output: tuple val(meta), path("*.fq.gz") , emit: reads tuple val(meta), path("*report.txt"), emit: log path "versions.yml" , emit: versions tuple val(meta), path("*.html"), emit: html optional true tuple val(meta), path("*.zip") , emit: zip optional true when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' // Calculate number of --cores for TrimGalore based on value of task.cpus // See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019 // See: https://github.com/nf-core/atacseq/pull/65 def cores = 1 if (task.cpus) { cores = (task.cpus as int) - 4 if (meta.single_end) cores = (task.cpus as int) - 3 if (cores < 1) cores = 1 if (cores > 4) cores = 4 } // Clipping presets have to be evaluated in the context of SE/PE def c_r1 = params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : '' def c_r2 = params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : '' def tpc_r1 = params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : '' def tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : '' // Added soft-links to original fastqs for consistent naming in MultiQC def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz trim_galore \\ $args \\ --cores $cores \\ --gzip \\ $c_r1 \\ $tpc_r1 \\ ${prefix}.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') cutadapt: \$(cutadapt --version) END_VERSIONS """ } else { """ [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz trim_galore \\ $args \\ --cores $cores \\ --paired \\ --gzip \\ $c_r1 \\ $c_r2 \\ $tpc_r1 \\ $tpc_r2 \\ ${prefix}_1.fastq.gz \\ ${prefix}_2.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') cutadapt: \$(cutadapt --version) END_VERSIONS """ } }