mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
4efa8da5c5
* controlfreec significance * move freec files to own subfolder * Fix meta.yml naming * Fix meta.yml naming * Fix linting * Forgot to refactor * forgot more refactoring * Too much refactoring on output paths * Too little refactoring here * update checksum
30 lines
1,013 B
Text
30 lines
1,013 B
Text
process CONTROLFREEC_ASSESSSIGNIFICANCE {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::control-freec=11.6" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
|
|
'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(cnvs), path(ratio)
|
|
|
|
output:
|
|
tuple val(meta), path("*.p.value.txt"), emit: bam
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
"""
|
|
cat /usr/local/bin/assess_significance.R | R --slave --args ${cnvs} ${ratio}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
|
|
END_VERSIONS
|
|
"""
|
|
}
|