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Code Issues Releases Packages Activity

fixed some issues

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This commit is contained in:
Nicolas Vannieuwkerke 2022-05-09 15:47:07 +02:00
parent d6dd4c2e2d
commit f6262b4a10
4 changed files with 12 additions and 10 deletions
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3
modules/rtgtools/vcfeval/main.nf
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@ -8,8 +8,9 @@ process RTGTOOLS_VCFEVAL {
'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }" 'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(bed) tuple val(meta), path(query_vcf), path(query_vcf_tbi)
tuple path(truth_vcf), path(truth_vcf_tbi) tuple path(truth_vcf), path(truth_vcf_tbi)
path(bed)
path(sdf) path(sdf)
output: output:

6
modules/rtgtools/vcfeval/meta.yml
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@ -40,9 +40,9 @@ input:
description: The BED file of the called VCF description: The BED file of the called VCF
pattern: "*.bed" pattern: "*.bed"
- sdf: - sdf:
type: folder/file type: file
description: The SDF (RTG Sequence Data File) of the reference genome. Can be a folder or a tar-zipped folder. description: The SDF (RTG Sequence Data File) folder of the reference genome
pattern: "*.{,tar.gz}" pattern: "*"
output: output:
- meta: - meta:

10
tests/modules/rtgtools/vcfeval/main.nf
View file

@ -11,7 +11,6 @@ workflow test_rtgtools_vcfeval {
[ id:'test' ], // meta map [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
] ]
truth = [ truth = [
@ -19,6 +18,8 @@ workflow test_rtgtools_vcfeval {
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true) file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
] ]
bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
compressed_sdf = [ compressed_sdf = [
[], [],
file(params.test_data['homo_sapiens']['genome']['genome_21_sdf']) file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
@ -31,7 +32,7 @@ workflow test_rtgtools_vcfeval {
}) })
RTGTOOLS_VCFEVAL ( input, truth, sdf ) RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
} }
workflow test_rtgtools_vcfeval_no_index { workflow test_rtgtools_vcfeval_no_index {
@ -40,7 +41,6 @@ workflow test_rtgtools_vcfeval_no_index {
[ id:'test' ], // meta map [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
[], [],
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
] ]
truth = [ truth = [
@ -48,6 +48,8 @@ workflow test_rtgtools_vcfeval_no_index {
[] []
] ]
bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
compressed_sdf = [ compressed_sdf = [
[], [],
file(params.test_data['homo_sapiens']['genome']['genome_21_sdf']) file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
@ -59,5 +61,5 @@ workflow test_rtgtools_vcfeval_no_index {
[folder] [folder]
}) })
RTGTOOLS_VCFEVAL ( input, truth, sdf ) RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
} }

1
tests/modules/rtgtools/vcfeval/test.yml
View file

@ -7,7 +7,6 @@
- path: output/rtgtools/test_results.txt - path: output/rtgtools/test_results.txt
md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4 md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4
- path: output/rtgtools/versions.yml - path: output/rtgtools/versions.yml
md5sum: 270ed7a5a8e347b251eb4aa2198f98e8
- name: rtgtools vcfeval test_rtgtools_vcfeval_no_index - name: rtgtools vcfeval test_rtgtools_vcfeval_no_index
command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_index -c tests/config/nextflow.config command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_index -c tests/config/nextflow.config