mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
f5d5926516
* Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
37 lines
1.5 KiB
Text
37 lines
1.5 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { STRELKA_GERMLINE } from '../../../../modules/strelka/germline/main.nf'
|
|
|
|
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_21_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
|
|
|
STRELKA_GERMLINE ( input, fasta, fai)
|
|
}
|
|
|
|
workflow test_strelka_germline_target_bed {
|
|
|
|
input = [
|
|
[ id:'test'], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
|
|
]
|
|
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
|
|
|
STRELKA_GERMLINE ( input, fasta, fai)
|
|
}
|
|
|