nf-core_modules/modules/cutadapt/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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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), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1'
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} else {
container 'quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1'
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}
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path('*.trim.fastq.gz'), emit: reads
tuple val(meta), path('*.log') , emit: log
path "versions.yml" , emit: versions
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script:
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
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(cutadapt --version)
END_VERSIONS
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"""
}