nf-core_modules/software/gatk4/applybqsr/main.nf

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'

params.options = [:]
options        = initOptions(params.options)

process GATK4_APPLYBQSR {
    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(bqsr_table)
    path fasta
    path fastaidx
    path dict
    path intervalsBed

    output:
    tuple val(meta), path("*.bam"), emit: bam
    path "*.version.txt"          , emit: version

    script:
    def software = getSoftwareName(task.process)
    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
    def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""

    """
    gatk ApplyBQSR \\
        -R $fasta \\
        -I $bam \\
        --bqsr-recal-file $bqsr_table \\
        $intervalsCommand \\
        -O ${prefix}.bam \\
        $options.args

    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
    """
}