mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
1363130410
removed a redundant input field from vcfanno Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
36 lines
1.3 KiB
Text
36 lines
1.3 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { UNTAR } from '../../../modules/untar/main.nf'
|
|
include { VCFANNO } from '../../../modules/vcfanno/main.nf'
|
|
|
|
workflow test_vcfanno {
|
|
|
|
input = [
|
|
[ id:'test_compressed', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
|
|
]
|
|
|
|
toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
|
|
resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ]
|
|
|
|
UNTAR ( resource_dir )
|
|
VCFANNO ( input, toml, UNTAR.out.untar.map{ it[1] } )
|
|
}
|
|
|
|
workflow test_vcfanno_uncompressed {
|
|
|
|
input = [
|
|
[ id:'test_uncompressed', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
|
|
[]
|
|
]
|
|
|
|
toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
|
|
resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ]
|
|
|
|
UNTAR ( resource_dir )
|
|
VCFANNO ( input, toml, UNTAR.out.untar.map{ it[1] } )
|
|
}
|