mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
1287ba48fe
* Update version & add intervals usage * Fix config when passing intervals as file * Use proper paths
36 lines
1.7 KiB
Text
36 lines
1.7 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { DEEPVARIANT } from '../../../modules/deepvariant/main.nf'
|
|
include { DEEPVARIANT as DEEPVARIANT_INTERVALS } from '../../../modules/deepvariant/main.nf'
|
|
|
|
workflow test_deepvariant {
|
|
|
|
bam_tuple_ch = Channel.of([ [ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
|
[]
|
|
])
|
|
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
|
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
|
|
DEEPVARIANT ( bam_tuple_ch, fasta, fai)
|
|
}
|
|
|
|
workflow test_deepvariant_cram_intervals {
|
|
|
|
cram_tuple_ch = Channel.of([[ 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'], checkIfExists: true)
|
|
])
|
|
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
|
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
|
|
DEEPVARIANT_INTERVALS ( cram_tuple_ch, fasta, fai)
|
|
}
|