adds conditional to allow testing

workflow/rules/common.smk

@@ -56,6 +56,15 @@ def get_targets(tool_name, samples=None):
     return flist
 
 
+def is_testing_mode():
+    "checks if testing dataset is used as input for the pipeline"
+
+    if ".test/" in str(PROJECT_PATH):
+        return True
+
+    return None
+
+
 #### configs from cli ####
 OUT_DIR = Path(config["out_dir"])
 PROJECT_NAME = config["project_name"]

workflow/rules/within_species_contamintation.smk

@@ -26,7 +26,7 @@ rule verifybamid:
     params:
         svd_prefix=lambda wildcards, input: input["svd"][0].replace(Path(input["svd"][0]).suffix, ""),
         out_prefix=lambda wildcards, output: output["ancestry"].replace(".Ancestry", ""),
-        sanity_check="TODO: Setup --DisableSanityCheck flag for testing dataset",
+        sanity_check="--DisableSanityCheck" if is_testing_mode() else "",
     threads: 4
     shell:
         r"""