Hack: directories must be local

- there is no way to handle input directory with remote URL

workflow/rules/common.smk

@@ -317,6 +317,9 @@ def cohortdir(fname):
 
 
 # handle Genes GFF
+if config.input["gff_directory"]:
+    assert is_local_file(config.input["gff_directory"]), f"ERROR: section 'input' property 'gff_directory' cannot be a remote URL {config.input['gff_directory']}.\nwhen not running V-pipe locally (e.g. snakedeploy) you need to either:\n- set it to empty''\n- copy to a local directory and specify that as the gff_directory"
+
 if (
     "genes_gff" in config.frameshift_deletions_checks
     and config.frameshift_deletions_checks["genes_gff"]