nf-core_modules/tests/software/bcftools/mpileup/main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { BCFTOOLS_MPILEUP } from '../../../../software/bcftools/mpileup/main.nf' addParams( options: ['args2': '--no-version --ploidy 1 --multiallelic-caller',
                                                                                                       'args3': '--no-version' ] )

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

    BCFTOOLS_MPILEUP ( input, fasta )
}