#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { QUALIMAP_BAMQCCRAM } from '../../../../modules/qualimap/bamqccram/main.nf'

workflow test_qualimap_bamqc {
    input   = [ [ id:'test', single_end:false ], // meta map
                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
              ]
    gff     = []
    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)

    QUALIMAP_BAMQCCRAM ( input, gff, fasta, fai )
}