mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
09acfad211
* added the module * updated test.yml * Update modules/gatk4/collectreadcounts/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * small fix * tests update * linting * tests update (again) Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
54 lines
2 KiB
Text
54 lines
2 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { GATK4_COLLECTREADCOUNTS } from '../../../../modules/gatk4/collectreadcounts/main.nf'
|
|
|
|
workflow test_gatk4_collectreadcounts_hdf5 {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
|
|
]
|
|
|
|
fasta = []
|
|
fai = []
|
|
dict = []
|
|
|
|
GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
|
|
}
|
|
|
|
workflow test_gatk4_collectreadcounts_tsv {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
|
|
]
|
|
|
|
fasta = []
|
|
fai = []
|
|
dict = []
|
|
|
|
GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
|
|
}
|
|
|
|
workflow test_gatk4_collectreadcounts_cram {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
|
|
]
|
|
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
|
|
|
GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
|
|
}
|
|
|