/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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
----------------------------------------------------------------------------------------
*/

//
// Sentieon alignment options
//

process {
    withName: '.*ALIGN_SENTIEON:.*' {
        ext.when = params.aligner.equals("sentieon")
    }

    withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_BWAMEM' {
        ext.args = { "-M -K 10000000 -R ${meta.read_group} " }
        ext.prefix = { "${meta.id}.sorted" }
    }

    withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DATAMETRICS' {
        ext.prefix = { "${meta.id}_datametrics" }
    }

    withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_READWRITER' {
        ext.prefix = { "${meta.id}_merged" }
    }

    withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_LOCUSCOLLECTOR' {
        ext.prefix = { "${meta.id}_locuscollector" }
    }

    withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP' {
        ext.args = { $params.rmdup ? "--rmdup" : '' }
        ext.prefix = { "${meta.id}_dedup" }
        publishDir = [
            enabled: !params.save_mapped_as_cram,
            path: { "${params.outdir}/alignment" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
        ]
    }

    withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_BQSR' {
        ext.prefix = { "${meta.id}_bqsr" }
    }
}
