mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
ffedf09b6e
* Fix typo * Revert to have target bed matched with sample info * Add comment on design decision
48 lines
2.4 KiB
Text
48 lines
2.4 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
|
|
|
|
workflow test_manta_germline {
|
|
input = [
|
|
[ id:'test'], // 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)],
|
|
[],[]
|
|
]
|
|
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)
|
|
|
|
MANTA_GERMLINE ( input, fasta, fai )
|
|
}
|
|
|
|
workflow test_manta_germline_target_bed {
|
|
input = [
|
|
[ id:'test'], // 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_gz'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], 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)
|
|
|
|
MANTA_GERMLINE ( input, fasta, fai )
|
|
}
|
|
|
|
workflow test_manta_germline_target_bed_jointcalling {
|
|
input = [
|
|
[ id:'test'], // meta map
|
|
[file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_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']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),],
|
|
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], 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)
|
|
|
|
MANTA_GERMLINE ( input, fasta, fai )
|
|
}
|