nf-core_modules/tests/modules/dastool/scaffolds2bin/main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf' addParams( options: [args: '--minContig 1500 --minCV 0.1 --minCVSum 0.1 --minClsSize 10 --minS 2'] )
include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' addParams( options: [:] )
include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf' addParams( options: [:] )

workflow test_dastool_scaffolds2bin {

    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_SCAFFOLDS2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
}