mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-26 23:43:19 -05:00
d27b7a6fda
* Add combinebrackenoutputs * Prettier and relax tests contains * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
25 lines
1.3 KiB
Text
25 lines
1.3 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { UNTAR } from '../../../../modules/untar/main.nf'
|
|
include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf'
|
|
include { BRACKEN_BRACKEN } from '../../../../modules/bracken/bracken/main.nf'
|
|
include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../../../modules/bracken/combinebrackenoutputs/main.nf'
|
|
|
|
workflow test_bracken_combinebrackenoutputs {
|
|
|
|
input = Channel.of(
|
|
[[ id:'test', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
|
|
[[ id:'test2', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
|
|
)
|
|
db = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
|
|
|
|
ch_db = UNTAR ( [[:], db] ).untar
|
|
.map { it[1] }
|
|
KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
|
|
BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
|
|
|
|
BRACKEN_COMBINEBRACKENOUTPUTS ( BRACKEN_BRACKEN.out.reports.map{it[1]}.collect() )
|
|
}
|
|
|