Add testcases for known sites

tests/test_sanity_checks.yml

@@ -39,3 +39,31 @@
       - "/very/unlikely/to/exist does not exist"
   tags:
     - sanity
+
+- name: test-known-sites-does-not-exist
+  command: >
+    snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
+    REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
+    ONETHOUSAND=Snakefile HAPMAP=Snakefile
+    SAMPLE_CONFIG=Snakefile
+    KNOWN_SITES=/very/unlikely/to/exist
+  exit_code: 1
+  stdout:
+    contains:
+      - "/very/unlikely/to/exist does not exist"
+  tags:
+    - sanity
+
+- name: test-known-sites-any-does-not-exist
+  command: >
+    snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
+    REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
+    ONETHOUSAND=Snakefile HAPMAP=Snakefile
+    SAMPLE_CONFIG=Snakefile
+    KNOWN_SITES=Snakefile,/very/unlikely/to/exist
+  exit_code: 1
+  stdout:
+    contains:
+      - "/very/unlikely/to/exist does not exist"
+  tags:
+    - sanity