nf-core_modules/modules/porechop/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PORECHOP {
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::porechop=0.2.4" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2"
} else {
container "quay.io/biocontainers/porechop:0.2.4--py38h8c62d01_2"
}
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.fastq.gz") , emit: reads
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
porechop \\
-i ${reads} \\
-t ${task.cpus} \\
${options.args} \\
-o ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( porechop --version )
END_VERSIONS
"""
}