nf-core_modules/modules/adapterremovalfixprefix/main.nf
James A. Fellows Yates 8c00897853
Add AdapterRemovalFixPrefix (#1424)
* Add AdapterRemovalFixPrefix

* Prettifying

Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
2022-03-21 11:26:12 +01:00

38 lines
1.1 KiB
Text

def VERSION = '0.05'
process ADAPTERREMOVALFIXPREFIX {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }"
input:
tuple val(meta), path(fastq)
output:
tuple val(meta), path("*.fq.gz"), emit: fixed_fastq
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if ("$fastq" == "${prefix}.fq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
"""
AdapterRemovalFixPrefix \\
$fastq \\
$args \\
| gzip > ${prefix}.fq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
adapterremovalfixprefix: $VERSION
END_VERSIONS
"""
}