main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { BWA_INDEX } from './modules/bwa/index/main.nf'
include { BWA_MEM   } from './modules/bwa/mem/main.nf'

def test_data_dir = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data"
genome_fasta = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta"
test_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_1.fastq.gz"

workflow {
    def meta = new CustomObject(id: 'test_1',
                                single_end: true,
                                read_group: "\"@RG\\tID:1\\tSM:sample\\tLB:rg_lb\\tPL:illumina\"",
                                r1: file(test_1_fastq_gz, checkIfExists: true))

    fasta = file(genome_fasta, checkIfExists: true)

    BWA_INDEX ( fasta )
    BWA_MEM ( meta, BWA_INDEX.out.index, false )
}