#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { GATK4_MUTECT2                       } from '../../../../modules/gatk4/mutect2/main.nf'
include { GATK4_MUTECT2 as GATK4_MUTECT2_PAIR } from '../../../../modules/gatk4/mutect2/main.nf'
include { GATK4_MUTECT2 as GATK4_MUTECT2_MITO } from '../../../../modules/gatk4/mutect2/main.nf'
include { GATK4_MUTECT2 as GATK4_MUTECT2_F1R2 } from '../../../../modules/gatk4/mutect2/main.nf'

workflow test_gatk4_mutect2_tumor_normal_pair {
    input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
                ],
              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
                ],
              []
            ]

    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)

    GATK4_MUTECT2_PAIR ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
}

workflow test_gatk4_mutect2_tumor_normal_pair_f1r2 {
    input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
                ],
              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
                ],
              []
            ]

    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)

    GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
}

workflow test_gatk4_mutect2_tumor_single {
    input = [ [ id:'test'], // meta map
              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
              []
            ]

    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)

    GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
}

workflow test_gatk4_mutect2_cram_input {
    input = [ [ id:'test'], // meta map
              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)],
              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)],
              []
            ]

    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)

    GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
}

workflow test_gatk4_mutect2_generate_pon {
    input = [ [ id:'test'], // meta map
              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
              []
            ]

    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)

    GATK4_MUTECT2 ( input, fasta, fai, dict, [], [], [], [] )
}

// mitochondria mode would ideally have some mitochondria test data
// but since the mitochondria settings only increase detection sensitivity
// we can use the chr22 data as a stand in as it is already a small dataset
// the extra variants detected compared to generate_pon shows the mode is working
workflow test_gatk4_mutect2_mitochondria {
    input = [ [ id:'test'], // meta map
              [ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam'], checkIfExists: true)],
              [ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam_bai'], checkIfExists: true)],
              [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]
            ]

    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)

    GATK4_MUTECT2_MITO ( input, fasta, fai, dict, [], [], [], [] )
}

workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
    input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
              [ "foo_parired.bam",
                "foo_parired2.bam"
                ],
              [ "foo_parired.bam.bai",
                "foo_parired2.bam.bai"
                ],
              []
            ]

    fasta = "genome.fasta"
    fai = "genome.fasta.fai"
    dict = "genome.fasta.dict"
    germline_resource = "genome_gnomAD.r2.1.1.vcf.gz"
    germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi"
    panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz"
    panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi"

    GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
}