mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
8d4373b4e8
* added bcftools convert * Update modules/bcftools/convert/main.nf Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> * updated test.yml * Update modules/bcftools/convert/main.nf Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> * added automatic output type detection * linting * removed a trailing whitespace Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
51 lines
1.6 KiB
Text
51 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_GVCF } from '../../../../modules/bcftools/convert/main.nf'
|
|
include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_BCF } from '../../../../modules/bcftools/convert/main.nf'
|
|
|
|
workflow test_bcftools_convert_gvcf {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
|
|
[]
|
|
]
|
|
|
|
bed = []
|
|
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
|
|
|
BCFTOOLS_CONVERT_GVCF ( input, bed, fasta )
|
|
}
|
|
|
|
workflow test_bcftools_convert_gvcf_bed {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true)
|
|
]
|
|
|
|
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
|
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
|
|
|
BCFTOOLS_CONVERT_GVCF ( input, bed, fasta )
|
|
}
|
|
|
|
workflow test_bcftools_convert_gvcf_to_bcf {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
|
|
[]
|
|
]
|
|
|
|
bed = []
|
|
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
|
|
|
BCFTOOLS_CONVERT_BCF ( input, bed, fasta )
|
|
}
|