nf-core_modules/software/cutadapt/main.nf
Jose Espinosa-Carrasco 572abb00b3
Remove def from module options definition in main (#270)
* Remove def from module options definition in main

* Fix bismark_deduplicate tests

* Fix bwameth_align tests

* Fixing gatk4 conda tests ("=" instead of ':' in build id)

* Same as previous commit (Fix gatk4 test)

* Fix qualimap bamqc test (no md5 check for pngs)

* Fix seqkit split2 tests. Changed to new test data

* Fix samtools tests. Some were missing initOptions include

* Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 12:16:43 +00:00

42 lines
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Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process CUTADAPT {
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), publish_id:meta.id) }
conda (params.enable_conda ? 'bioconda::cutadapt=3.2' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/cutadapt:3.2--py38h0213d0e_0'
} else {
container 'quay.io/biocontainers/cutadapt:3.2--py38h0213d0e_0'
}
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path('*.trim.fastq.gz'), emit: reads
tuple val(meta), path('*.log') , emit: log
path '*.version.txt' , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def trimmed = meta.single_end ? "-o ${prefix}.trim.fastq.gz" : "-o ${prefix}_1.trim.fastq.gz -p ${prefix}_2.trim.fastq.gz"
"""
cutadapt \\
--cores $task.cpus \\
$options.args \\
$trimmed \\
$reads \\
> ${prefix}.cutadapt.log
echo \$(cutadapt --version) > ${software}.version.txt
"""
}