call_snv_deepvariant_parabricks.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
----------------------------------------------------------------------------------------
*/

//
// SNV calling options - parabricks deepvariant
//

process {

    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:.*' {
        ext.when = params.variant_caller.equals("parabricks_deepvariant")
    }

    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:PARABRICKS_DEEPVARIANT' {
        ext.args = { [
            '--gvcf',
            params.analysis_type.toUpperCase() == 'WES' ? '--use-wes-model' : '',
            (meta.sex == 1) ?
                (params.genome == 'GRCh37' ? '--haploid-contigs X,Y' : '--haploid-contigs chrX,chrY')
                : ''
        ].findAll { it }.join(' ').trim() }

        ext.prefix = { "${meta.id}_parabricks_deepvar" }

        label = 'process_gpu'
    }

    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:GLNEXUS' {
        ext.args = '--config DeepVariant_unfiltered'
    }

    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:SPLIT_MULTIALLELICS_PB' {
        ext.args = '--output-type z --multiallelics -both'
    }

    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:REMOVE_DUPLICATES_PB' {
        ext.args = '--output-type z --rm-dup none'
        ext.prefix = { "${meta.id}_split_rmdup" }
    }

    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:ADD_VARCALLER_TO_BED' {
        ext.args2   = '-s 1 -b 2 -e 3'
    }

    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:BCFTOOLS_ANNOTATE' {
        ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z"
        ext.prefix = { "${meta.id}_split_rmdup_info" }
    }
}