mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
5e18e36895
* Fixes for PR 371 * Fix tags * Add md5sum * Add md5sums for stringtie * Fix tests for modules where subtool = build * Fix pytest_software name conflicts * Change _ to / in test.yml tags * Nope...that didnt work * Fix sequenzautils/bam2seqz tests
29 lines
1.1 KiB
Text
29 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { STRINGTIE as STRINGTIE_FORWARD } from '../../../software/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward' ] )
|
|
include { STRINGTIE as STRINGTIE_REVERSE } from '../../../software/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse' ] )
|
|
|
|
/*
|
|
* Test with forward strandedness
|
|
*/
|
|
workflow test_stringtie_forward {
|
|
input = [ [ id:'test', strandedness:'forward' ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
|
|
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
|
|
|
|
STRINGTIE_FORWARD ( input, gtf )
|
|
}
|
|
|
|
/*
|
|
* Test with reverse strandedness
|
|
*/
|
|
workflow test_stringtie_reverse {
|
|
input = [ [ id:'test', strandedness:'reverse' ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
|
]
|
|
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
|
|
|
|
STRINGTIE_REVERSE ( input, gtf )
|
|
}
|