nf-core_modules/modules/gatk4/baserecalibrator/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GATK4_BASERECALIBRATOR {
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(bam), path(bai)
path fasta
path fastaidx
path dict
path intervalsBed
path knownSites
path knownSites_tbi
output:
tuple val(meta), path("*.table"), emit: table
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ')
"""
gatk BaseRecalibrator \
-R $fasta \
-I $bam \
$sitesCommand \
$intervalsCommand \
$options.args \
-O ${prefix}.table
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}