comment for auto mode (9ce4f95e) · Commits · github_fork / Universc

launch_universc.sh

+4 −2

Original line number	Diff line number	Diff line
		@@ -877,7 +877,7 @@ elif ! [[ $mem =~ $int ]] && [[ $setup == "false" ]]; then
		fi

		#check if chemistry matches expected input
		#allow "auto" for 10x
		#allow "auto" only for 10x
		if [[ "$technology" != "10x" ]]; then
		#use SC3Pv3 (umi length 12)
		if [[ $umilength -ge 11 ]] && [[ "$chemistry" == "SC3Pv1" ]] && [[ "$chemistry" == "SC3Pv2" ]]; then
		@@ -920,6 +920,7 @@ fi

		#####Get barcode/UMI length#####
		barcode_default=16
		# default UMI depends on chemistry selected above (unless auto is used for 10x)
		if [[ "$chemistry" == *"v2" ]]; then
		umi_default=10
		elif [[ "$chemistry" == *"v3" ]]; then
		@@ -933,6 +934,7 @@ barcodelength=""
		umilength=""
		if [[ "$technology" == "10x" ]]; then
		barcodelength=16
		#set umi length to default (no conversion so auto detection will work)
		umilength=10
		umi_default=10
		elif [[ "$technology" == "celseq" ]]; then
		@@ -1289,7 +1291,7 @@ else
		fi

		#remove adapter from SureCell (and correct phase blocks)
		if [[ "$technology" == "surecell" ]];
		if [[ "$technology" == "surecell" ]]; then
		for convFile in "${convFiles[@]}"; do
		#remove phase blocks and linkers
		sed -E '