nf-core_modules/tests/modules/dastool/dastool/main.nf
James A. Fellows Yates 8ce6810787
Update DASTool to 1.1.4 (#1471)
* fix: remove left-over unnecessary code

* Update DASTool

* Fix tests

* Fix test.ymls

* Fix container build version

* Make tests less strict to account for variability

* Apply suggestions from code review

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Add missing description

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-04-01 11:33:07 +02:00

33 lines
1.5 KiB
Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
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'
include { DASTOOL_DASTOOL } from '../../../../modules/dastool/dastool/main.nf'
workflow test_dastool_dastool {
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")
Channel.of([ [ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)])
.join( DASTOOL_FASTATOCONTIG2BIN.out.fastatocontig2bin )
.set {input_dastool}
DASTOOL_DASTOOL ( input_dastool, [], [] )
}