call_sv_MT.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
----------------------------------------------------------------------------------------
*/

//
// Call SV in mitochondria
//

process {

    withName: '.*CALL_SV_MT:MT_DELETION' {
        ext.args = '-s --insert-size 16000'
        ext.prefix = { "${meta.id}_mitochondria_deletions" }
    }

    withName: '.*CALL_SV_MT:SALTSHAKER_CALL' {
        ext.args = '--blacklist'
    }

    withName: '.*CALL_SV_MT:SALTSHAKER_CLASSIFY' {
        ext.args = { [
            "--blacklist --vcf",
            "--dominant-fraction ${params.saltshaker_dominant_fraction}",
            "--radius ${params.saltshaker_group_radius}",
            "--high-het ${params.saltshaker_high_heteroplasmy}",
            "--multiple-threshold ${params.saltshaker_multiple_threshold}",
            "--noise ${params.saltshaker_noise_threshold}"
        ].join(' ') }
    }

    withName: '.*CALL_SV_MT:SALTSHAKER_TO_HTML' {
        ext.prefix = { "${meta.id}.saltshaker_classify" }
    }

    withName: '.*CALL_SV_MT:SALTSHAKER_PLOT' {
        ext.args = '--blacklist --genes'
    }

    withName: '.*CALL_SV_MT:SVDB_MERGE' {
        ext.prefix = { "${meta.id}_saltshaker" }
    }

}