mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
57 lines
2 KiB
Text
57 lines
2 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { GATK4_COLLECTSVEVIDENCE } from '../../../../modules/gatk4/collectsvevidence/main.nf'
|
||
|
|
|
||
|
|
workflow test_gatk4_collectsvevidence_cram {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ 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),
|
||
|
|
[],
|
||
|
|
[]
|
||
|
|
]
|
||
|
|
|
||
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||
|
|
|
||
|
|
GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_gatk4_collectsvevidence_bam {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ 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 = []
|
||
|
|
fasta_fai = []
|
||
|
|
dict = []
|
||
|
|
|
||
|
|
GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_gatk4_collectsvevidence_allele_count {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ 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),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
|
||
|
|
fasta = []
|
||
|
|
fasta_fai = []
|
||
|
|
dict = []
|
||
|
|
|
||
|
|
GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
|
||
|
|
}
|