mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
23 lines
924 B
Text
23 lines
924 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { MANTA_CONVERTINVERSION } from '../../../../modules/manta/convertinversion/main.nf'
|
|
include { MANTA_TUMORONLY } from '../../../../modules/manta/tumoronly/main.nf'
|
|
|
|
workflow test_manta_convertinversion {
|
|
|
|
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),
|
|
[], []
|
|
]
|
|
|
|
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)
|
|
|
|
MANTA_TUMORONLY ( input, fasta, fai )
|
|
|
|
MANTA_CONVERTINVERSION ( MANTA_TUMORONLY.out.tumor_sv_vcf, fasta )
|
|
}
|