#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { UNTAR } from '../../../../software/untar/main.nf'
include { ARTIC_MINION } from '../../../../software/artic/minion/main.nf' addParams(  fast5_dir: true, sequencing_summary: true, artic_minion_medaka_model:false )

workflow test_artic_minion {

    input              = [ [ id:'test', single_end:false ], // meta map
                             file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
    fast5_tar          = [ file(params.test_data['sarscov2']['nanopore']['fast5_tar_gz'], checkIfExists: true) ]
    sequencing_summary = [ file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true) ]
    fasta              = [ file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists: true) ]
    bed                = [ file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists: true) ]
    dummy_file         = [ ]

    fast5_dir = UNTAR ( fast5_tar ).untar

    ARTIC_MINION ( input, fast5_dir, sequencing_summary, fasta, bed, dummy_file, 'nCoV-2019', '3')
}