mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
f126d980d7
* inital commit * added meta.yaml info * add initial logic for featurecounts test * add args and change SE/PE to strandedness for featurecounts test * added tests to pytest * added test.yml * removed GTF flag in options * corrected test meta params * meta yaml corrected tool info * update test.yml * fix lint errors meta.yml Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
35 lines
No EOL
1.3 KiB
Text
35 lines
No EOL
1.3 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { SUBREAD_FEATURECOUNTS } from '../../../../software/subread/featurecounts/main.nf' addParams( options: [args:'-t CDS'] )
|
|
|
|
workflow test_subread_featurecounts_forward {
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
|
|
|
|
SUBREAD_FEATURECOUNTS ( input )
|
|
}
|
|
|
|
workflow test_subread_featurecounts_reverse {
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:true, strandedness:'reverse' ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
|
|
|
|
SUBREAD_FEATURECOUNTS ( input )
|
|
}
|
|
|
|
workflow test_subread_featurecounts_unstranded {
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
|
|
|
|
SUBREAD_FEATURECOUNTS ( input )
|
|
} |