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

// MPILEUP

process {

    withName: 'CAT_MPILEUP' {
        publishDir       = [
            enabled: false
        ]
    }

    withName: 'BCFTOOLS_MPILEUP' {
        ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.bcftools" : "${meta.id}_${intervals.simpleName}.bcftools" }
        ext.when   = { params.tools && params.tools.split(',').contains('mpileup') }
        ext.args2  = "--multiallelic-caller"
        ext.args3  = "-i 'count(GT==\"RR\")==0'" // only report non homozygous reference variants
        publishDir = [
            mode: params.publish_dir_mode,
            path: { "${params.outdir}/variant_calling/bcftools/${meta.id}/" },
            pattern: "*{vcf.gz,vcf.gz.tbi}",
            saveAs: { meta.num_intervals > 1 ? null : it }
        ]
    }

    withName: 'MERGE_BCFTOOLS_MPILEUP' {
        ext.prefix       = {"${meta.id}.bcftools"}
        publishDir       = [
            mode: params.publish_dir_mode,
            path: { "${params.outdir}/variant_calling/bcftools/${meta.id}/" },
            pattern: "*{vcf.gz,vcf.gz.tbi}"
        ]
    }

    withName: 'SAMTOOLS_MPILEUP' {
        ext.when   = { params.tools && params.tools.split(',').contains('controlfreec') }
        publishDir = [
            enabled: false
        ]

    }

// PAIR_VARIANT_CALLING
    if (params.tools && params.tools.split(',').contains('controlfreec')) {
        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_MPILEUP:SAMTOOLS_MPILEUP' {
            ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.normal" : "${meta.id}_${intervals.simpleName}.normal" }
        }

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_MPILEUP:CAT_MPILEUP' {
            ext.prefix = { "${meta.id}.normal.mpileup.gz" }
        }

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_NORMAL:SAMTOOLS_MPILEUP' {
            ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.normal" : "${meta.id}_${intervals.simpleName}.normal" }
        }

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_NORMAL:CAT_MPILEUP' {
            ext.prefix = { "${meta.id}.normal.mpileup.gz" }
        }

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_TUMOR:SAMTOOLS_MPILEUP' {
            ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.tumor" : "${meta.id}_${intervals.simpleName}.tumor" }
        }

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_TUMOR:CAT_MPILEUP' {
            ext.prefix = { "${meta.id}.tumor.mpileup.gz" }
        }

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_MPILEUP:SAMTOOLS_MPILEUP' {
            ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.tumor" : "${meta.id}_${intervals.simpleName}.tumor" }
        }

        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_MPILEUP:CAT_MPILEUP' {
            ext.prefix = { "${meta.id}.tumor.mpileup.gz" }
        }
    }
}
