nf-core_modules/modules/porechop/main.nf
2022-02-04 09:53:32 +01:00

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process PORECHOP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' :
'quay.io/biocontainers/porechop:0.2.4--py39h7cff6ad_2' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.fastq.gz"), emit: reads
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
porechop \\
-i $reads \\
-t $task.cpus \\
$args \\
-o ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
porechop: \$( porechop --version )
END_VERSIONS
"""
}