#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { ANTISMASH_ANTISMASHLITE                  } from '../../../../modules/antismash/antismashlite/main.nf'
include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
include { GUNZIP as GUNZIP1 } from '../../../../modules/gunzip/main.nf'
include { GUNZIP as GUNZIP2 } from '../../../../modules/gunzip/main.nf'
include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf'
include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf'
include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf'

workflow test_antismashlite {
    genome_fna = [
        [ id:'test' ],
        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
    ]

    genome_gff = [
        [],
        file(params.test_data['bacteroides_fragilis']['genome']['genome_gff_gz'], checkIfExists: true)
    ]

    antismash_css = [
        [],
        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
    ]

    antismash_detection = [
        [],
        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
    ]

    antismash_modules = [
        [],
        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
    ]

    GUNZIP1 ( genome_fna )
    GUNZIP2 ( genome_gff )
    UNTAR1 ( antismash_css )
    UNTAR2 ( antismash_detection )
    UNTAR3 ( antismash_modules )
    ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
    ANTISMASH_ANTISMASHLITE ( GUNZIP1.out.gunzip, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir, GUNZIP2.out.gunzip.map{ it[1] } )
}