mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
aa32a8a72e
* initiated files for calculate contamination * pushing local repo to remote * created script, filled in meta yml, created tests and test yml. local checks passing, needs repo side test data * added option and tests for outputting optional segmentation file * saving for test push * versions updated, test data added * Update main.nf * fixed versions info, should report correctly now * small update to main.nf outputs formatting * Apply suggestions from code review * Update test_data.config * Apply suggestions from code review Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
47 lines
1.8 KiB
Text
47 lines
1.8 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process GATK4_CALCULATECONTAMINATION {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
|
|
|
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
|
|
} else {
|
|
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(pileup), path(matched)
|
|
val segmentout
|
|
|
|
output:
|
|
tuple val(meta), path('*.contamination.table') , emit: contamination
|
|
tuple val(meta), path('*.segmentation.table') , optional:true, emit: segmentation
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def matched_command = matched ? " -matched ${matched} " : ''
|
|
def segment_command = segmentout ? " -segments ${prefix}.segmentation.table" : ''
|
|
"""
|
|
gatk CalculateContamination \\
|
|
-I $pileup \\
|
|
$matched_command \\
|
|
-O ${prefix}.contamination.table \\
|
|
$segment_command \\
|
|
$options.args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|