nf-core_modules/modules/snapaligner/paired/main.nf
Matthias De Smet 09125979cc
Tool/snap aligner paired (#1509)
* first commit

* edit main.nf

* edit tests

* run prettier

* fix test

* indent script

* Update modules/snapaligner/paired/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/snapaligner/paired/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* fix version nr

* update meta

* fix versions

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-12 11:02:10 +02:00

41 lines
1.1 KiB
Text

process SNAPALIGNER_PAIRED {
tag '$meta.id'
label 'process_high'
conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1':
'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }"
input:
tuple val(meta), path(reads)
path index
output:
tuple val(meta), path("*.bam"), emit: bam
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}"
"""
mkdir -p index
mv $index index/
snap-aligner paired \\
index \\
${reads.join(" ")} \\
-o -bam ${prefix}.bam \\
-t ${task.cpus} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //;s/.\$//')
END_VERSIONS
"""
}