#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { ULTRA_PIPELINE } from '../../../../modules/ultra/pipeline/main.nf' addParams( options: [:] )
include { GUNZIP         } from '../../../../modules/gunzip/main.nf'         addParams( options: [:] )
include { GFFREAD        } from '../../../../modules/gffread/main.nf'        addParams( options: [args: "--sort-alpha --keep-genes -T", suffix: "_sorted"] )

workflow test_ultra_pipeline {

    fastq  = file(params.test_data['homo_sapiens']['pacbio']['hifi']        , checkIfExists: true)
    gtf    = file(params.test_data['homo_sapiens']['genome']['genome_gtf']  , checkIfExists: true)
    genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)

    GUNZIP ( fastq )
    GFFREAD ( gtf )

    GUNZIP
        .out
        .gunzip
        .map { [ [ id:'test', single_end:false ], it ] }
        .set { input }

    ULTRA_PIPELINE ( input, genome, GFFREAD.out.gtf )
}