mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 00:02:04 +00:00
36 lines
1.6 KiB
Text
36 lines
1.6 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf' addParams( options: [:] )
|
||
|
|
|
||
|
|
workflow test_manta_germline {
|
||
|
|
input = [
|
||
|
|
[ id:'test'], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], 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)
|
||
|
|
bed = []
|
||
|
|
bed_tbi = []
|
||
|
|
|
||
|
|
MANTA_GERMLINE ( input, fasta, fai, bed, bed_tbi )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_manta_germline_target_bed {
|
||
|
|
input = [
|
||
|
|
[ id:'test'], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], 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)
|
||
|
|
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
|
||
|
|
bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
|
||
|
|
|
||
|
|
MANTA_GERMLINE ( input, fasta, fai, bed, bed_tbi )
|
||
|
|
}
|