From 98560bebf8ad234f6a8ccdc552302bbfc2fcb83c Mon Sep 17 00:00:00 2001 From: Ivan Blagoev Topolsky Date: Thu, 27 Jul 2023 01:13:46 +0200 Subject: [PATCH] Hack: directories must be local - there is no way to handle input directory with remote URL --- workflow/rules/common.smk | 3 +++ 1 file changed, 3 insertions(+) diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index f673c269..0a1cd0ca 100644 --- a/workflow/rules/common.smk +++ b/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"]