process FASTP { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' : 'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }" input: tuple val(meta), path(reads) val save_trimmed_fail val save_merged output: tuple val(meta), path('*.trim.fastq.gz') , emit: reads tuple val(meta), path('*.json') , emit: json tuple val(meta), path('*.html') , emit: html tuple val(meta), path('*.log') , emit: log path "versions.yml" , emit: versions tuple val(meta), path('*.fail.fastq.gz') , optional:true, emit: reads_fail tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' // Added soft-links to original fastqs for consistent naming in MultiQC def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : '' """ [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz fastp \\ --in1 ${prefix}.fastq.gz \\ --out1 ${prefix}.trim.fastq.gz \\ --thread $task.cpus \\ --json ${prefix}.fastp.json \\ --html ${prefix}.fastp.html \\ $fail_fastq \\ $args \\ 2> ${prefix}.fastp.log cat <<-END_VERSIONS > versions.yml "${task.process}": fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g") END_VERSIONS """ } else { def fail_fastq = save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : '' def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : '' """ [ ! -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 fastp \\ --in1 ${prefix}_1.fastq.gz \\ --in2 ${prefix}_2.fastq.gz \\ --out1 ${prefix}_1.trim.fastq.gz \\ --out2 ${prefix}_2.trim.fastq.gz \\ --json ${prefix}.fastp.json \\ --html ${prefix}.fastp.html \\ $fail_fastq \\ $merge_fastq \\ --thread $task.cpus \\ --detect_adapter_for_pe \\ $args \\ 2> ${prefix}.fastp.log cat <<-END_VERSIONS > versions.yml "${task.process}": fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g") END_VERSIONS """ } }