From daf61e7bd3b2b10162cbec140af91feba92ae79f Mon Sep 17 00:00:00 2001 From: dpryan79 Date: Mon, 3 Sep 2018 21:13:58 +0200 Subject: [PATCH] Fix #245 --- snakePipes/workflows/RNA-seq/RNA-seq | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/snakePipes/workflows/RNA-seq/RNA-seq b/snakePipes/workflows/RNA-seq/RNA-seq index 8e5ab3d9c..0c175b721 100755 --- a/snakePipes/workflows/RNA-seq/RNA-seq +++ b/snakePipes/workflows/RNA-seq/RNA-seq @@ -138,6 +138,10 @@ def main(): args.SNPfile = os.path.abspath(args.SNPfile) args.Nmasked_index = os.path.abspath(args.Nmasked_index) modeTemp = args.mode.split(",") + validModes = set(["alignment", "alignment-free", "deeptools_qc"]) + for mode in modeTemp: + if mode not in validModes: + sys.exit("{} is not a valid mode!\n".format(mode)) # deeptools_qc requires alignment as input if "deeptools_qc" in modeTemp and "alignment" not in modeTemp: args.mode = "{},alignment".format(args.mode)