#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { GATK4_MERGEBAMALIGNMENT } from '../../../../software/gatk4/mergebamalignment/main.nf' addParams( options: [:] )

workflow test_gatk4_mergebamalignment {
    def input = []
    input = [ [ id:'test' ], // meta map
              file("${launchDir}/tests/data/genomics/sarscov2/bam/test_single_end.bam", checkIfExists: true) ]
    unmapped = file("${launchDir}/tests/data/genomics/sarscov2/bam/test_unaligned.bam", checkIfExists: true)
    fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
    dict = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.dict", checkIfExists: true)

    GATK4_MERGEBAMALIGNMENT ( input, unmapped, fasta, dict )
}