#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { BISCUIT_INDEX  } from '../../../../modules/biscuit/index/main.nf'
include { BISCUIT_PILEUP } from '../../../../modules/biscuit/pileup/main.nf'

workflow test_biscuit_pileup {

    input = [ [ id:'test' ], // meta map
        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)],
        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)],    
	[], //tumor bam 
	[] //tumor bai
        ]
    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)

    BISCUIT_INDEX ( fasta )
    BISCUIT_PILEUP ( input, BISCUIT_INDEX.out.index )

}

workflow test_biscuit_pileup_somatic {

    input = [ [ id:'test' ], // meta map
        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)    
        ]
    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)

    BISCUIT_INDEX ( fasta )
    BISCUIT_PILEUP ( input, BISCUIT_INDEX.out.index )

}