support longer UMIs with SC3Pv3 chemistry and warn from non-UMI kits (24ea5d0e) · Commits · github_fork / Universc

launch_universc.sh

+25 −4

Original line number	Diff line number	Diff line
		@@ -456,6 +456,7 @@ if [[ "$technology" == "dropseq" ]] \|\| [[ "$technology" == "drop-seq" ]]; then
		fi
		if [[ "$technology" == "icell8" ]] \|\| [[ "$technology" == "icell-8" ]]; then
		echo "Running with iCELL8 parameters (version 3 with UMIs)"
		echo "*WARNING: iCELL8 settings should only be used for kits that have UMIs*"
		technology="icell8"
		fi
		if [[ "$technology" == "indrop-v1" ]] \|\| [[ "$technology" == "indrops-v1" ]] \|\| [[ "$technology" == "indropv1" ]] \|\| [[ "$technology" == "indropsv1" ]]; then
		@@ -486,6 +487,7 @@ if [[ "$technology" == "scrubseq" ]] \|\| [[ "$technology" == "scrub-seq" ]]; then
		fi
		if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smart-seq" ]] \|\| [[ "$technology" == "smartseq2" ]] \|\| [[ "$technology" == "smart-seq2" ]] \|\| [[ "$technology" == "smartseq2-umi" ]] \|\| [[ "$technology" == "smart-seq2-umi" ]] \|\| [[ "$technology" == "smartseq3" ]] \|\| [[ "$technology" == "smart-seq3" ]]; then
		echo "Running with Smart-Seq3 parameters (version 3 with UMIs)"
		echo "*WARNING: Smart-Seq settings should only be used for kits that have UMIs*"
		technology="smartseq"
		fi

		@@ -816,10 +818,22 @@ elif ! [[ $mem =~ $int ]] && [[ $setup == "false" ]]; then
		fi

		#check if chemistry matches expected input
		if [[ "$chemistry" != "SC3Pv3" ]] && [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then
		#allow "auto" for 10x
		if [[ "$technology" != "10x" ]]; then
		#use SC3Pv3 (umi length 12)
		if [[ $umilength -ge 11 ]] && [[ "$chemistry" == "SC3Pv1" ]] && [[ "$chemistry" == "SC3Pv2" ]]; then
		echo "Using 10x version 3 chemistry to support longer UMIs"
		chemistry="SC3Pv3"
		else
		#use SC3Pv2 (umi length 10)
		echo "Using 10x version 2 chemistry to support UMIs"
		chemistry="SC3Pv2"
		fi
		if [[ "$chemistry" != "SC3Pv1" ]] && [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC3Pv3" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then
		echo "Error: option --chemistry must be SC3Pv3, SC3Pv2, SC5P-PE , or SC5P-R2"
		exit 1
		fi
		fi

		#checking if jobmode matches expected input
		if [[ "$jobmode" != "local" ]] && [[ "$jobmode" != "sge" ]] && [[ "$jobmode" != "lsf" ]] && [[ "$jobmode" != *"template" ]]; then
		@@ -847,7 +861,12 @@ fi

		#####Get barcode/UMI length#####
		barcode_default=16
		if [[ "$chemistry" == *"v2" ]]; then
		umi_default=10
		elif [[ "$chemistry" == *"v3" ]]; then
		umi_default=12
		fi

		totallength=`echo $((${barcode_default}+${umi_default}))`

		#barcode and umi lengths given by options
		@@ -856,6 +875,7 @@ umilength=""
		if [[ "$technology" == "10x" ]]; then
		barcodelength=16
		umilength=10
		umi_default=10
		elif [[ "$technology" == "celseq" ]]; then
		barcodelength=6
		umilength=6
		@@ -887,6 +907,7 @@ else
		umilength=`echo $technology \| cut -f$((${custom})) -d'_'`
		fi


		#adjustment lengths
		barcodeadjust=`echo $(($barcodelength-$barcode_default))`
		umiadjust=`echo $(($umilength-$umi_default))`

Admin message