nf-core_modules/modules/trimgalore/main.nf
Harshil Patel c5235a983d
nf-core modules bump-versions for all modules (#630)
* Add blacklist of modules that shouldn't be updated to .nf-core.yml

* nf-core modules bump-versions for all modules

* Remove TODO statements identified by linting

* Fix md5sums for failing tests

* Fix more tests
2021-07-28 09:10:44 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process TRIMGALORE {
tag "$meta.id"
label 'process_high'
publishDir "${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::trim-galore=0.6.7' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0"
} else {
container "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 "*.version.txt" , emit: version
tuple val(meta), path("*.html"), emit: html optional true
tuple val(meta), path("*.zip") , emit: zip optional true
script:
// 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 ${params.three_prime_clip_r2}" : ''
// Added soft-links to original fastqs for consistent naming in MultiQC
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
trim_galore \\
$options.args \\
--cores $cores \\
--gzip \\
$c_r1 \\
$tpc_r1 \\
${prefix}.fastq.gz
echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//' > ${software}.version.txt
"""
} 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 \\
$options.args \\
--cores $cores \\
--paired \\
--gzip \\
$c_r1 \\
$c_r2 \\
$tpc_r1 \\
$tpc_r2 \\
${prefix}_1.fastq.gz \\
${prefix}_2.fastq.gz
echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//' > ${software}.version.txt
"""
}
}