nf-core_modules/modules/prinseqplusplus/main.nf
James A. Fellows Yates f1c5384c31
Add PRINSEQPLUSPLUS (#1481)
* fix: remove left-over unnecessary code

* Add prinseq++

* Remove last todo

* Fix tests due to variability of output FASTQs (reads can be ordered differently between runs)

* Apply suggestions from code review
2022-04-03 16:06:22 +02:00

61 lines
1.9 KiB
Text

process PRINSEQPLUSPLUS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/prinseq-plus-plus:1.2.3--hc90279e_1':
'quay.io/biocontainers/prinseq-plus-plus:1.2.3--hc90279e_1' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*_good_out*.fastq.gz") , emit: good_reads
tuple val(meta), path("*_single_out*.fastq.gz"), optional: true, emit: single_reads
tuple val(meta), path("*_bad_out*.fastq.gz") , optional: true, emit: bad_reads
tuple val(meta), path("*.log") , emit: log
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 (meta.single_end) {
"""
prinseq++ \\
-threads $task.cpus \\
-fastq ${reads} \\
-out_name ${prefix} \\
-out_gz \\
-VERBOSE 1 \\
$args \\
| tee ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
prinseqplusplus: \$(echo \$(prinseq++ --version | cut -f 2 -d ' ' ))
END_VERSIONS
"""
} else {
"""
prinseq++ \\
-threads $task.cpus \\
-fastq ${reads[0]} \\
-fastq2 ${reads[1]} \\
-out_name ${prefix} \\
-out_gz \\
-VERBOSE 1 \\
$args \\
| tee ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
prinseqplusplus: \$(echo \$(prinseq++ --version | cut -f 2 -d ' ' ))
END_VERSIONS
"""
}
}