mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
6720d88f4e
* Updated container versions for fgbio groupreadsbyumi and callmolecularconsensusreads * Corrected fgbio call container, trying to fix fgbio group tests * Removed incorrect line * Changed tmp-dir to . * Update modules/fgbio/groupreadsbyumi/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/fgbio/fastqtobam/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Added callmol and sortbam * fixed typo in callmol container Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
41 lines
1.2 KiB
Text
41 lines
1.2 KiB
Text
process FGBIO_FASTQTOBAM {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
|
|
'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
val read_structure
|
|
|
|
output:
|
|
tuple val(meta), path("*_umi_converted.bam"), emit: umibam
|
|
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}"
|
|
"""
|
|
|
|
fgbio \\
|
|
--tmp-dir=. \\
|
|
FastqToBam \\
|
|
-i $reads \\
|
|
-o "${prefix}_umi_converted.bam" \\
|
|
--read-structures $read_structure \\
|
|
--sample $meta.id \\
|
|
--library $meta.id \\
|
|
$args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|