#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { LEEHOM } from '../../../modules/leehom/main.nf' addParams( options: [:] )
include { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf'  addParams( options: [args: "-f4 -b"] )

workflow test_leehom_bam {

    input = [ [ id:'test', single_end:false ], // meta map
              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]

    fasta = []

    SAMTOOLS_VIEW ( input, fasta )
    LEEHOM ( SAMTOOLS_VIEW.out.bam )
}

workflow test_leehom_se_fq {

    input = [ [ id:'test', single_end:true ], // meta map
              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]

    LEEHOM ( input )
}

workflow test_leehom_pe_fq {

    input = [ [ id:'test', single_end:false ], // meta map
              [
                  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
                  file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
              ] ]

    LEEHOM ( input )
}