nf-core_modules/tests/modules/cooler/cload/main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { COOLER_CLOAD }                       from '../../../../modules/cooler/cload/main.nf'
include { COOLER_CLOAD as COOLER_CLOAD_PAIRS } from '../../../../modules/cooler/cload/main.nf'
include { COOLER_CLOAD as COOLER_CLOAD_TABIX } from '../../../../modules/cooler/cload/main.nf'
include { COOLER_DUMP }                        from '../../../../modules/cooler/dump/main.nf'
include { COOLER_DUMP as COOLER_DUMP_PAIRS}    from '../../../../modules/cooler/dump/main.nf'
include { COOLER_DUMP as COOLER_DUMP_TABIX}    from '../../../../modules/cooler/dump/main.nf'

workflow test_cooler_cload_pairix {

    input = [ [ id:'test_pairix', single_end:false ], // meta map
             file(params.test_data['generic']['cooler']['test_pairix_pair_gz'], checkIfExists: true),
             file(params.test_data['generic']['cooler']['test_pairix_pair_gz_px2'], checkIfExists: true)]

    sizes    = file(params.test_data['generic']['cooler']['hg19_chrom_sizes'], checkIfExists: true)
    bin_size = 2000000

    COOLER_CLOAD ( input, bin_size, sizes )
    COOLER_DUMP(COOLER_CLOAD.out.cool.map{[it[0], it[2]]}, [])

}

workflow test_cooler_cload_pairs {

    input = [ [ id:'test_pairs', single_end:false ], // meta map
             file(params.test_data['generic']['cooler']['test_pairs_pair'], checkIfExists: true),
             []]

    sizes    = file(params.test_data['generic']['cooler']['hg19_chrom_sizes'], checkIfExists: true)
    bin_size = 2000000

    COOLER_CLOAD_PAIRS ( input, bin_size, sizes )
    COOLER_DUMP_PAIRS(COOLER_CLOAD_PAIRS.out.cool.map{[it[0], it[2]]}, [])

}

workflow test_cooler_cload_tabix {

    input = [ [ id:'test_tabix', single_end:false ], // meta map
             file(params.test_data['generic']['cooler']['test_tabix_pair_gz'], checkIfExists: true),
             file(params.test_data['generic']['cooler']['test_tabix_pair_gz_tbi'], checkIfExists: true)]

    sizes    = file(params.test_data['generic']['cooler']['hg19_chrom_sizes'], checkIfExists: true)
    bin_size = 2000000

    COOLER_CLOAD_TABIX ( input, bin_size, sizes )
    COOLER_DUMP_TABIX(COOLER_CLOAD_TABIX.out.cool.map{[it[0], it[2]]}, [])

}