mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
57 lines
2 KiB
Text
57 lines
2 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { SVTK_STANDARDIZE } from '../../../../modules/svtk/standardize/main.nf'
|
||
|
|
include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
|
||
|
|
|
||
|
|
workflow test_svtk_standardize {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ], // 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)
|
||
|
|
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
|
||
|
|
MANTA_GERMLINE(
|
||
|
|
input,
|
||
|
|
fasta,
|
||
|
|
fasta_fai
|
||
|
|
)
|
||
|
|
|
||
|
|
SVTK_STANDARDIZE (
|
||
|
|
MANTA_GERMLINE.out.diploid_sv_vcf,
|
||
|
|
fasta_fai
|
||
|
|
)
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_svtk_standardize_no_contigs {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ], // 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)
|
||
|
|
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
|
||
|
|
MANTA_GERMLINE(
|
||
|
|
input,
|
||
|
|
fasta,
|
||
|
|
fasta_fai
|
||
|
|
)
|
||
|
|
|
||
|
|
SVTK_STANDARDIZE (
|
||
|
|
MANTA_GERMLINE.out.diploid_sv_vcf,
|
||
|
|
[]
|
||
|
|
)
|
||
|
|
}
|