mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
32 lines
1.6 KiB
Text
32 lines
1.6 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/gatk4/getpileupsummaries/main.nf' addParams( options: [:] )
|
||
|
|
|
||
|
|
workflow test_gatk4_getpileupsummaries_just_variants {
|
||
|
|
|
||
|
|
input = [ [ id:'test' ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) ,
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ]
|
||
|
|
|
||
|
|
variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
|
||
|
|
variants_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
|
||
|
|
sites = []
|
||
|
|
|
||
|
|
GATK4_GETPILEUPSUMMARIES ( input , variants , variants_idx , sites )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_gatk4_getpileupsummaries_separate_sites {
|
||
|
|
|
||
|
|
input = [ [ id:'test' ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) ,
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ]
|
||
|
|
|
||
|
|
variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
|
||
|
|
variants_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
|
||
|
|
sites = file( "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.interval_list" , checkIfExists: true)
|
||
|
|
|
||
|
|
GATK4_GETPILEUPSUMMARIES ( input , variants , variants_idx , sites )
|
||
|
|
}
|