nf-core_modules/tests/modules/svtk/standardize/main.nf
nvnieuwk bf09fdf892
new module: svtk/standardize (#2031)
* new module: svtk/standardize

* linting

* fixed tests
2022-09-08 15:03:08 +02:00

56 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,
[]
)
}