mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
83 lines
3.1 KiB
Text
83 lines
3.1 KiB
Text
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
|
|
"""
|
|
}
|
|
}
|