#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { UNZIP as UNZIP_MALT        } from '../../../modules/unzip/main.nf' addParams( options: [:] )
include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/unzip/main.nf' addParams( options: [:] )
include { MALT_BUILD  } from  '../../../modules/malt/build/main.nf' addParams( options: [:] )
include { MALT_RUN    } from '../../../modules/malt/run/main.nf' addParams( options: [:] )
include { MALTEXTRACT } from '../../../modules/maltextract/main.nf' addParams( options: [args: "-f def_anc"] )
include { AMPS        } from '../../../modules/amps/main.nf' addParams( options: [:] )


workflow test_amps {

    fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
    gff = []
    seq_type = "DNA"
    map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true)
    input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
    mode = "BlastN"
    taxon_list = file(params.test_data['sarscov2']['genome']['taxon_list_txt'], checkIfExists: true)
    ncbi_dir = file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true)
    filter = "def_anc"

    UNZIP_MALT ( map_db )
    UNZIP_MALTEXTRACT ( ncbi_dir )
    MALT_BUILD ( fastas, seq_type, gff, UNZIP_MALT.out.unzipped_archive )
    MALT_RUN ( input, mode, MALT_BUILD.out.index )
    MALTEXTRACT ( MALT_RUN.out.rma6, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive)

    AMPS ( MALTEXTRACT.out.results, taxon_list, filter )
}