nf-core_modules/tests/modules/vcfanno/main.nf
James A. Fellows Yates e080f4c8ac
Untar unzip meta (#1408)
* fix: remove left-over unnecessary code

* Adds support for meta lists for unzip and untar

* Fix test inputs

* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple

* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple

* Fix MALTEXTRACT/AMPS

* Fix further modules

* Fix cellranger

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-03-21 14:49:28 +01:00

41 lines
1.5 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)
]
input_2 = [ [ id:'test_compressed', single_end:false ], // meta map
[] ]
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, input_2, toml, UNTAR.out.untar.map{ it[1] } )
}
workflow test_vcfanno_uncompressed {
input = [ [ id:'test_uncompressed', single_end:false ], // meta map
[] ,[] ]
input_2 = [
[ 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, input_2, toml, UNTAR.out.untar.map{ it[1] } )
}