Merge pull request #58 from teojcryan/fix/custom-tax-bug

Fix: validate --custom-tax argument to prevent TypeError

Author: farchaab

mess/workflow/rules/preflight/functions.smk

@@ -212,7 +212,7 @@ if "input_tsv" not in tsv_cache:
 else:
     tsv_df = tsv_cache["input_tsv"]
 
-if config.args.custom_tax:
+if isinstance(config.args.custom_tax, str):
     if "custom_tax_df" not in tsv_cache:
         custom_tax_df = pd.read_csv(config.args.custom_tax, sep="\t")
         tsv_cache["custom_tax_df"] = custom_tax_df

mess/workflow/rules/preflight/setup.smk

@@ -51,7 +51,7 @@ if not os.path.exists(os.path.join(TAXONKIT, "names.dmp")):
 
 
 RANKS = config.args.ranks
-if config.args.custom_tax:
+if isinstance(config.args.custom_tax, str):
     RANKS = ",".join(list(custom_tax_df.columns[1:]))
     TAXONKIT = os.path.join(TAXONKIT, "custom")