call_snv.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Config file for defining DSL2 per module options and publishing paths
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Available keys to override module options:
        ext.args            = Additional arguments appended to command in module.
        ext.args2           = Second set of arguments appended to command in module (multi-tool modules).
        ext.args3           = Third set of arguments appended to command in module (multi-tool modules).
        ext.prefix          = File name prefix for output files.
        ext.when            = Conditional clause
----------------------------------------------------------------------------------------
*/

process {

    withName: '.*CALL_SNV:GATK4_SELECTVARIANTS' {
        ext.args   = { "--exclude-intervals ${params.mito_name}" }
        ext.prefix = { "${meta.id}_snv" }
        publishDir = [
            path: { "${params.outdir}/call_snv/genome" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
        ]
    }

    withName: '.*CALL_SNV:BCFTOOLS_CONCAT' {
        ext.args   = { "--write-index=tbi" }
        ext.prefix = { "${meta.id}_mt_and_nuclear_snvs" }
        publishDir = [
            enabled: params.concatenate_snv_calls,
            path: { "${params.outdir}/call_snv/concatenated_calls" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
        ]
    }
}