nf-core_modules/tests/modules/strelka/germline/main.nf
FriederikeHanssen 754db250a0
Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912)
* remove params statement

* add manta/somatic module

* fix strelka target bed thing

* removing checksums should make this pass

* Update modules/manta/somatic/main.nf

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* fix indentation

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2021-10-27 16:14:52 +02:00

36 lines
1.7 KiB
Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { STRELKA_GERMLINE } from '../../../../modules/strelka/germline/main.nf' addParams( options: [:] )
workflow test_strelka_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)
target_bed = []
target_bed_tbi = []
STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi )
}
workflow test_strelka_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)
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
target_bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi )
}