disable barcode checks for custom whitelists (84b2e0e3) · Commits · github_fork / Universc

launch_universc.sh

+4 −0

Original line number	Diff line number	Diff line
		@@ -2324,6 +2324,8 @@ if [[ $lock -eq 0 ]]; then
		fi
		sed -i "s/ raise NoChemistryFoundException/ return best_chem #raise NoChemistryFoundException/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py
		sed -i "s/ (100\.0 \* best_frac/ #(100.0 * best_frac/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py
		sed -i "s/return msg/return None #msg/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py
		sed -i "s/return msg/return None #msg/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/check.py
		else
		if [[ $verbose ]]; then
		echo "restore detect chemistry check..."
		@@ -2331,6 +2333,8 @@ if [[ $lock -eq 0 ]]; then
		#restore detect chemistry check for custom whitelist
		sed -i "s/ return best_chem \#raise NoChemistryFoundException/ raise NoChemistryFoundException/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py
		sed -i "s/ \#(100\.0 \* best_frac/ (100.0 * best_frac/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py
		sed -i "s/return None #msg/return msg/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py
		sed -i "s/return None #msg/return msg/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/check.py
		fi

		#determine last barcode and UMI