correct passing auto chemistry to detect 10x v3 (5ef95054) · Commits · github_fork / Universc

launch_universc.sh

+10 −11

Original line number	Diff line number	Diff line
		@@ -2027,7 +2027,15 @@ fi
		#allow "auto" only for 10x
		if [[ "$technology" != "10x" ]]; then
		#use SC3Pv3 (umi length 12)
		if [[ $umilength -ge 11 ]]; then
		if [[ "$chemistry" != "auto" ]];then
		#use automatic chemistry detection
		echo "Detecting 10x chemistry automatically"
		chemistry="auto"
		#do not convert UMI
		umi_default=12
		umilength=${umi_default}
		umiadjust=0
		elif [[ $umilength -ge 11 ]]; then
		if [[ "$chemistry" == "SC3Pv1" ]] \|\| [[ "$chemistry" == "SC3Pv2" ]]; then
		echo "Using 10x version 3 chemistry to support longer UMIs"
		chemistry="SC3Pv3"
		@@ -2038,14 +2046,6 @@ if [[ "$technology" != "10x" ]]; then
		echo "Using 10x version 2 chemistry to support UMIs"
		chemistry="SC3Pv2"
		umi_default=10
		elif [[ "$chemistry" != "auto" ]];then
		#use automatic chemistry detection
		echo "Detecting 10x chemistry automatically"
		chemistry="auto"
		#do not convert UMI
		umi_default=12
		umilength=${umi_default}
		umiadjust=0
		fi
		if [[ "$chemistry" != "threeprime" ]] && [[ "$chemistry" != "fiveprime" ]] && [[ "$chemistry" != "SC3Pv1" ]] && [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC3Pv3" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R1" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then
		echo "Error: option --chemistry must be SC3Pv3, SC3Pv2, SC5P-PE, SC5P-R1, or SC5P-R2"
		@@ -2064,7 +2064,6 @@ if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smartseq3" ]] \|\| [[
		exit 1
		fi
		fi
		chemistry="SC3Pv2" #####KAI REMEMBER TO REMOVE THIS#####
		##########


		@@ -3512,7 +3511,7 @@ if [[ $verbose ]]; then
		echo $chemistry
		fi

		if [[ $chemistry == "SC5P"* ]] \|\| [[ $chemistry == "five"* ]]; then
		if [[ $chemistry == "SC5P"* ]] \|\| [[ $chemistry == "five"* ]] \|\| [[ $chemistry == "auto" ]]; then
		r=""
		else
		r="--r1-length=$totallength"

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