mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
572abb00b3
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
48 lines
1.5 KiB
Text
48 lines
1.5 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process GATK4_MERGEVCFS {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
|
|
|
conda (params.enable_conda ? 'bioconda::gatk4=4.1.9.0' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
|
|
} else {
|
|
container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0'
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(vcfs)
|
|
path(ref_dict)
|
|
val use_ref_dict
|
|
|
|
output:
|
|
tuple val(meta), path('*.vcf.gz') , emit: vcf
|
|
path '*.version.txt' , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
|
|
// Make list of VCFs to merge
|
|
def input = ""
|
|
for (vcf in vcfs) {
|
|
input += " I=${vcf}"
|
|
}
|
|
def ref = use_ref_dict ? "D=${ref_dict}" : ""
|
|
"""
|
|
gatk MergeVcfs \\
|
|
$input \\
|
|
O=${prefix}.merged.vcf.gz \\
|
|
$ref \\
|
|
$options.args
|
|
|
|
gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
|
|
"""
|
|
}
|