mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
26 lines
963 B
Text
26 lines
963 B
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { ULTRA_PIPELINE } from '../../../../modules/ultra/pipeline/main.nf' addParams( options: [:] )
|
||
|
|
include { GUNZIP } from '../../../../modules/gunzip/main.nf' addParams( options: [:] )
|
||
|
|
include { GFFREAD } from '../../../../modules/gffread/main.nf' addParams( options: [args: "--sort-alpha --keep-genes -T", suffix: "_sorted"] )
|
||
|
|
|
||
|
|
workflow test_ultra_pipeline {
|
||
|
|
|
||
|
|
fastq = file(params.test_data['homo_sapiens']['pacbio']['hifi'] , checkIfExists: true)
|
||
|
|
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'] , checkIfExists: true)
|
||
|
|
genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
|
||
|
|
GUNZIP ( fastq )
|
||
|
|
GFFREAD ( gtf )
|
||
|
|
|
||
|
|
GUNZIP
|
||
|
|
.out
|
||
|
|
.gunzip
|
||
|
|
.map { [ [ id:'test', single_end:false ], it ] }
|
||
|
|
.set { input }
|
||
|
|
|
||
|
|
ULTRA_PIPELINE ( input, genome, GFFREAD.out.gtf )
|
||
|
|
}
|