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https://github.com/MillironX/nf-core_modules.git
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7e8ad56688
* 1882 FASTP now supports interleaved FASTQ files Changes: - single_end FASTP pipes the FASTQ file - Using args, it can be configured for interleaved in `--interleaved_in` - Out is automatically interleaved if input is paired end. - Removed md5sum checks for FASTQ files as compression seemed to cause differences - Instead, we check inside the FASTQ files for content. Relates to #1882 Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
79 lines
3 KiB
Text
79 lines
3 KiB
Text
process FASTP {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
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'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
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input:
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tuple val(meta), path(reads)
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val save_trimmed_fail
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val save_merged
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output:
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tuple val(meta), path('*.fastp.fastq.gz') , optional:true, emit: reads
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tuple val(meta), path('*.json') , emit: json
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tuple val(meta), path('*.html') , emit: html
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tuple val(meta), path('*.log') , emit: log
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path "versions.yml" , emit: versions
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tuple val(meta), path('*.fail.fastq.gz') , optional:true, emit: reads_fail
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tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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// Added soft-links to original fastqs for consistent naming in MultiQC
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def prefix = task.ext.prefix ?: "${meta.id}"
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// Use single ended for interleaved. Add --interleaved_in in config.
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if (meta.single_end) {
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def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
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"""
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[ ! -f ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
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cat ${prefix}.fastq.gz \\
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| fastp \\
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--stdin \\
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--stdout \\
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--in1 ${prefix}.fastq.gz \\
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--thread $task.cpus \\
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--json ${prefix}.fastp.json \\
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--html ${prefix}.fastp.html \\
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$fail_fastq \\
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$args \\
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2> ${prefix}.fastp.log \\
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| gzip -c > ${prefix}.fastp.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
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END_VERSIONS
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"""
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} else {
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def fail_fastq = save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
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def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
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"""
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[ ! -f ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
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[ ! -f ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
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fastp \\
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--in1 ${prefix}_1.fastq.gz \\
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--in2 ${prefix}_2.fastq.gz \\
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--out1 ${prefix}_1.fastp.fastq.gz \\
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--out2 ${prefix}_2.fastp.fastq.gz \\
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--json ${prefix}.fastp.json \\
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--html ${prefix}.fastp.html \\
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$fail_fastq \\
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$merge_fastq \\
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--thread $task.cpus \\
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--detect_adapter_for_pe \\
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$args \\
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2> ${prefix}.fastp.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
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END_VERSIONS
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"""
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}
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}
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