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getpileupsummaries requires intervals files

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Rike 2022-05-12 16:51:17 +02:00
parent f40cfefc08
commit b3bd55da76
2 changed files with 0 additions and 25 deletions
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15
tests/modules/gatk4/getpileupsummaries/main.nf
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@ -4,21 +4,6 @@ nextflow.enable.dsl = 2
include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/gatk4/getpileupsummaries/main.nf' include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/gatk4/getpileupsummaries/main.nf'
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_21_vcf_gz'], checkIfExists: true)
variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
fasta = []
fai = []
dict = []
GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi )
}
workflow test_gatk4_getpileupsummaries_separate_sites { workflow test_gatk4_getpileupsummaries_separate_sites {

10
tests/modules/gatk4/getpileupsummaries/test.yml
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@ -1,13 +1,3 @@
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_just_variants
command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_just_variants -c tests/config/nextflow.config
tags:
- gatk4/getpileupsummaries
- gatk4
files:
- path: output/gatk4/test.pileups.table
md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
- path: output/gatk4/versions.yml
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites
command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config
tags: tags: