nf-core_modules/tests/modules/stringtie/merge/main.nf
Harshil Patel 3c5492b4a3
Fix more version commands (#750)
* Fix outstanding tests

* Fix more version commands

* Fix remaining modules
2021-09-28 06:56:27 +01:00

46 lines
1.4 KiB
Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [:] )
include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf' addParams( options: [:] )
/*
* Test with forward strandedness
*/
workflow test_stringtie_forward_merge {
input = [
[ id:'test', strandedness:'forward' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE ( input, annotation_gtf )
STRINGTIE
.out
.transcript_gtf
.map { it -> it[1] }
.set { stringtie_gtf }
STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
}
/*
* Test with reverse strandedness
*/
workflow test_stringtie_reverse_merge {
input = [
[ id:'test', strandedness:'reverse' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE ( input, annotation_gtf )
STRINGTIE
.out
.transcript_gtf
.map { it -> it[1] }
.set { stringtie_gtf }
STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
}