#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { GUNZIP } from '../../../modules/gunzip/main.nf'
include { PRODIGAL } from '../../../modules/prodigal/main.nf'
include { DEEPBGC_DOWNLOAD } from '../../../../modules/deepbgc/download/main.nf'
include { DEEPBGC_PIPELINE } from '../../../../modules/deepbgc/pipeline/main.nf'

workflow test_deepbgc_pipeline_gbk {

    input = [
        [ id:'test_gbk', single_end:false ], // meta map
        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
    ]

    DEEPBGC_DOWNLOAD ()
    GUNZIP ( input )
    PRODIGAL ( GUNZIP.out.gunzip, 'gbk' )
    DEEPBGC_PIPELINE ( PRODIGAL.out.gene_annotations, DEEPBGC_DOWNLOAD.out.db )
}

workflow test_deepbgc_pipeline_fa {

    input = [
        [ id:'test_fa', single_end:false ], // meta map
        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
    ]

    DEEPBGC_DOWNLOAD ()
    GUNZIP ( input )
    DEEPBGC_PIPELINE ( GUNZIP.out.gunzip, DEEPBGC_DOWNLOAD.out.db )
}