From 2c276748badde9a700ab8dc1703a4e0c4e291bea Mon Sep 17 00:00:00 2001 From: chapmanb Date: Fri, 14 Jul 2017 04:24:39 -0400 Subject: [PATCH] effects: avoid lookup issues with non-CWL snpEff --- bcbio/variation/effects.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bcbio/variation/effects.py b/bcbio/variation/effects.py index be4e5fe46..fd563478b 100644 --- a/bcbio/variation/effects.py +++ b/bcbio/variation/effects.py @@ -276,7 +276,7 @@ def get_db(data): snpeff_base_dir = None if snpeff_db: snpeff_base_dir = utils.get_in(data, ("reference", "snpeff")) - if not isinstance(snpeff_base_dir, basestring) and os.path.isdir(snpeff_base_dir): + if not (isinstance(snpeff_base_dir, basestring) and os.path.isdir(snpeff_base_dir)): snpeff_base_dir = utils.get_in(data, ("reference", "snpeff", snpeff_db)) if not snpeff_base_dir: # We need to mask '.' characters for CWL/WDL processing, check for them here