Add testing to vcf-to-varda

test/test-integration.yml

+- name: test-integration-GIAB-chrM
+  tags:
+    - integration
+  command: >
+    snakemake
+    --configfile test/config/config-GIAB-chrM.json
+    --use-singularity
+    --singularity-args ' --containall --bind /tmp'
+    --notemp
+    --cores 1
+    16699289/varda/16699289_coverage.varda
+    16699289/varda/16699289_variants.varda
+  files:
+    - path: 16699289/varda/16699289_coverage.varda
+    - path: 16699289/varda/16699289_variants.varda
+
+- name: test-integration-trim-alt-exclude-uncalled
+  tags:
+    - integration
+  command: >
+    snakemake
+    --configfile test/config/config-noalt-uncalled.json
+    --use-singularity
+    --singularity-args ' --containall --bind /tmp'
+    --notemp
+    --cores 1
+    16699289/varda/16699289_trimmed.vcf
+  files:
+    - path: 16699289/varda/16699289_trimmed.vcf
+      must_not_contain:
+          - "chrM\t150\t.\tT\tC"
+          - "chrM\t152\t.\tT\tC"
+      contains:
+          - "chrM\t73\t.\tG\tA"
+          - "chrM\t150\t.\tT\t."
+          - "chrM\t152\t.\tT\t."
+          - "chrM\t195\t.\tC\tT"
+
+- name: test-integration-multiallelic
+  tags:
+    - integration
+  command: >
+    snakemake
+    --configfile test/config/config-multiallelic.json
+    --use-singularity
+    --singularity-args ' --containall --bind /tmp'
+    --notemp
+    --cores 1
+    16699289/varda/16699289_variants_ucsc.varda
+  files:
+    - path: 16699289/varda/16699289_trimmed.vcf
+      must_not_contain:
+          - "chrM\t195\t.\tC\tT,*"
+          - "chrM\t410\t.\tA\tC,G"
+          - "chrM\t2261\t.\tC\tT,CATTTT"
+      contains:
+          - "chrM\t195\t.\tC\t*"
+          - "chrM\t410\t.\tA\tC"
+          - "chrM\t2261\t.\tC\tT"
+    - path: 16699289/varda/16699289_single.vcf
+      must_not_contain:
+          - "chrM\t1581\t.\tA\tC,G"
+      contains:
+          - "chrM\t1581\t.\tA\tC"
+          - "chrM\t1581\t.\tA\tG"
+    - 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/varda/16699289_variants_ucsc.varda
+
+- name: test-integration-GIAB-chrM-coverage
+  tags:
+    - integration
+  command: >
+    snakemake
+    --configfile test/config/config-GIAB-chrM.json
+    --use-singularity
+    --singularity-args ' --containall --bind /tmp'
+    --notemp
+    --cores 1
+    16699289/varda/16699289_coverage.varda
+  files:
+    - path: 16699289/varda/16699289_coverage.varda
+      contains:
+          - "NC_012920.1\t0\t16571\t2"