mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
43 lines
1.3 KiB
Text
43 lines
1.3 KiB
Text
process ELPREP_MERGE {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0':
|
|
'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bam)
|
|
|
|
output:
|
|
tuple val(meta), path("output/**.{bam,sam}") , 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}"
|
|
def suffix = args.contains("--output-type sam") ? "sam" : "bam"
|
|
def single_end = meta.single_end ? " --single-end" : ""
|
|
|
|
"""
|
|
# create directory and move all input so elprep can find and merge them before splitting
|
|
mkdir input
|
|
mv ${bam} input/
|
|
|
|
elprep merge \\
|
|
input/ \\
|
|
output/${prefix}.${suffix} \\
|
|
$args \\
|
|
${single_end} \\
|
|
--nr-of-threads $task.cpus
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|