Add testing to vcf-to-varda

test/test-integration.yml

@@ -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"