#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { GUNZIP                                } from '../../../../modules/gunzip/main.nf'
include { METABAT2_METABAT2                     } from '../../../../modules/metabat2/metabat2/main.nf'
include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS  } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
include { DASTOOL_FASTATOCONTIG2BIN                 } from '../../../../modules/dastool/fastatocontig2bin/main.nf'

workflow test_dastool_fastatocontig2bin {

    input_depth = [ [ id:'test', single_end:false ], // meta map
              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]

    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )

    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
        .map { it -> [[ id:'test', single_end:false ], it] }
        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
        .set { input_metabat2 }

    METABAT2_METABAT2 ( input_metabat2 )

    DASTOOL_FASTATOCONTIG2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
}

workflow test_dastool_fastatocontig2bin_ungzipped {

    input_depth = [ [ id:'test', single_end:false ], // meta map
              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]


    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )

    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
        .map { it -> [[ id:'test', single_end:false ], it] }
        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
        .set { input_metabat2 }

    METABAT2_METABAT2 ( input_metabat2 )

    // TODO test unzipped input files
    ch_input_2_fastatocontig2bin = GUNZIP( METABAT2_METABAT2.out.fasta  ).gunzip

    DASTOOL_FASTATOCONTIG2BIN ( ch_input_2_fastatocontig2bin, "fa")
}