/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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   = When to run the module.
----------------------------------------------------------------------------------------
*/

// CNVKIT

process {

// PREPARE REFERENCE CNVKIT
    withName: 'CNVKIT_ANTITARGET' {
        ext.when         = { params.tools && params.tools.split(',').contains('cnvkit') }
        publishDir       = [
            enabled: params.save_reference,
            mode: params.publish_dir_mode,
            path: { "${params.outdir}/reference/cnvkit" },
            pattern: "*{bed}"
        ]
    }

    withName: 'CNVKIT_REFERENCE' {
        ext.prefix       = "cnvkit"
        ext.when         = { params.tools && params.tools.split(',').contains('cnvkit') && !params.cnvkit_reference }
        publishDir       = [
            enabled: params.save_reference,
            mode: params.publish_dir_mode,
            path: { "${params.outdir}/reference/cnvkit" },
            pattern: "*{cnn}"
        ]
    }

    // CNVKIT
    withName: 'CNVKIT_BATCH' {
        ext.args         = { params.wes ? "--method hybrid --diagram --scatter" : "--method wgs --diagram --scatter" }
        ext.when         = { params.tools && params.tools.split(',').contains('cnvkit') }
        publishDir       = [
            mode: params.publish_dir_mode,
            path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" },
            pattern: "*{bed,cnn,cnr,cns,pdf,png}"
        ]
    }
}
