mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
fd5f6f5f4f
* revert changes to modules * fix tests * fix kraken2 * fix untar * fix cat * add blank lines * fix typo
51 lines
1.4 KiB
Text
51 lines
1.4 KiB
Text
process TIDDIT_COV {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' :
|
|
'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bam)
|
|
path fasta
|
|
|
|
output:
|
|
tuple val(meta), path("*.tab"), optional: true, emit: cov
|
|
tuple val(meta), path("*.wig"), optional: true, emit: wig
|
|
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 reference = fasta ? "--ref $fasta" : ""
|
|
"""
|
|
tiddit \\
|
|
--cov \\
|
|
-o $prefix \\
|
|
$args \\
|
|
--bam $bam \\
|
|
$reference
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
|
|
stub:
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
touch ${prefix}.wig
|
|
touch ${prefix}.tab
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|