#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { TBPROFILER_PROFILE as TBPROFILER_PROFILE_ILLUMINA } from '../../../../modules/tbprofiler/profile/main.nf' addParams( options: [args: '--platform illumina'] )
include { TBPROFILER_PROFILE as TBPROFILER_PROFILE_NANOPORE} from '../../../../modules/tbprofiler/profile/main.nf' addParams( options: [args: '--platform nanopore'] )

workflow test_tbprofiler_profile_illumina {
    
    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) ] ]

    TBPROFILER_PROFILE_ILLUMINA ( input )
}


workflow test_tbprofiler_profile_nanopore {
    
    input = [ [ id:'test', single_end:true ], // meta map
              file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]

    TBPROFILER_PROFILE_NANOPORE ( input )
}