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Add testing to vcf-to-varda

Merged Add testing to vcf-to-varda
devel into master
Merged van den Berg requested to merge devel into master
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test/test-integration.yml
+ 13
− 12
@@ -8,10 +8,11 @@
--singularity-args ' --containall --bind /tmp'
--notemp
--cores 1
16699289_coverage.varda 16699289_variants.varda
16699289/varda/16699289_coverage.varda
16699289/varda/16699289_variants.varda
files:
- path: 16699289_coverage.varda
- path: 16699289_variants.varda
- path: 16699289/varda/16699289_coverage.varda
- path: 16699289/varda/16699289_variants.varda
- name: test-trim-alt-exclude-uncalled
tags:
@@ -23,9 +24,9 @@
--singularity-args ' --containall --bind /tmp'
--notemp
--cores 1
16699289_trimmed.vcf
16699289/varda/16699289_trimmed.vcf
files:
- path: 16699289_trimmed.vcf
- path: 16699289/varda/16699289_trimmed.vcf
must_not_contain:
- "chrM\t150\t.\tT\tC"
- "chrM\t152\t.\tT\tC"
@@ -45,9 +46,9 @@
--singularity-args ' --containall --bind /tmp'
--notemp
--cores 1
16699289_variants_ucsc.varda
16699289/varda/16699289_variants_ucsc.varda
files:
- path: 16699289_trimmed.vcf
- path: 16699289/varda/16699289_trimmed.vcf
must_not_contain:
- "chrM\t195\t.\tC\tT,*"
- "chrM\t410\t.\tA\tC,G"
@@ -56,14 +57,14 @@
- "chrM\t195\t.\tC\t*"
- "chrM\t410\t.\tA\tC"
- "chrM\t2261\t.\tC\tT"
- path: 16699289_single.vcf
- path: 16699289_no_alt_star.vcf
- path: 16699289/varda/16699289_single.vcf
- path: 16699289/varda/16699289_no_alt_star.vcf
must_not_contain:
- "chrM\t195\t.\tC\t*"
contains:
- "chrM\t152\t.\tT\tC"
- "chrM\t410\t.\tA\tC"
- path: 16699289_variants_ucsc.varda
- path: 16699289/varda/16699289_variants_ucsc.varda
- name: test-integration-GIAB-chrM-coverage
tags:
@@ -75,8 +76,8 @@
--singularity-args ' --containall --bind /tmp'
--notemp
--cores 1
16699289_coverage.varda
16699289/varda/16699289_coverage.varda
files:
- path: 16699289_coverage.varda
- path: 16699289/varda/16699289_coverage.varda
contains:
- "NC_012920.1\t0\t16571\t2"