nf-core_modules/modules/gatk4/createsomaticpanelofnormals/main.nf
GCJMackenzie 3c8ca3fec4
Createsomaticpanelofnormals (#859)
* files created for createsompon, script written, meta written, still needs tests

* updated to 2.0.0 method input, however this requires a genomicsDB input now

* script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests

* versions updated, issue with test data not able to download directory

* updated tests to include repo-side data

* Apply suggestions from code review

* Update modules/gatk4/createsomaticpanelofnormals/main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 19:30:14 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GATK4_CREATESOMATICPANELOFNORMALS {
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(genomicsdb)
path fasta
path fastaidx
path dict
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
gatk \\
CreateSomaticPanelOfNormals \\
-R $fasta \\
-V gendb://$genomicsdb \\
-O ${prefix}.vcf.gz \\
$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
"""
}