nf-core_modules/modules/fastp/main.nf
Harshil Patel 7b3315591a
Remove def software lines and emit versions channel as plural (#780)
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names
2021-10-01 14:04:56 +01:00

82 lines
3.3 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process FASTP {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::fastp=0.20.1' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0'
} else {
container 'quay.io/biocontainers/fastp:0.20.1--h8b12597_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
script:
// Added soft-links to original fastqs for consistent naming in MultiQC
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${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 \\
$options.args \\
2> ${prefix}.fastp.log
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(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 \\
$options.args \\
2> ${prefix}.fastp.log
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS
"""
}
}