nf-core_modules/tests/software/minimap2/align/main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { MINIMAP2_ALIGN } from '../../../../software/minimap2/align/main.nf' addParams( options: [:] )

workflow test_minimap2_align_single_end {
    input = [ [ id:'test', single_end:true ], // meta map
              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
            ]
    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

    MINIMAP2_ALIGN ( input, fasta )
}

workflow test_minimap2_align_paired_end {
    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) ]
            ]
    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

    MINIMAP2_ALIGN ( input, fasta )
}