nf-core_modules/tests/modules/gatk4/collectsvevidence/main.nf
2022-09-09 10:58:47 +02:00

56 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 )
}