minor changes for pipeline-specific modifications (ff51a6e2) · Commits · github_fork / Universc

launch_universc.sh

+28 −28

Original line number	Diff line number	Diff line
		@@ -1426,8 +1426,9 @@ else
		echo " barcodes: ${barcodeadjust}bps at its head"
		echo " UMIs: ${umiadjust}bps at its tail"

		#for CEL-Seq2 swap barcode and UMI
		if [[ "$technology" == "sciseq" ]]; then
		echo " making technology-specific modifications ..."
		#CEL-Seq2: swap barcode and UMI
		if [[ "$technology" == "celseq2" ]]; then
		for convFile in "${convFiles[@]}"; do
		#swap UMI and barcode
		sed -E '2~2s/(.{6})(.{6})/\2\1/' $convFile > ${crIN}/.temp
		@@ -1435,7 +1436,7 @@ else
		done
		fi

		#remove adapter from inDrops see here for details:
		#inDrops: remove adapter (see links below for details)
		## https://github.com/BUStools/bustools/issues/4
		## https://teichlab.github.io/scg_lib_structs/methods_html/inDrop.html
		if [[ "$technology" == "indrop-v1" ]] \|\| [[ "$technology" == "indrop-v2" ]]; then
		@@ -1454,7 +1455,7 @@ else
		done
		fi

		#remove adapter from QuartzSeq
		#QuartzSeq: remove adapter
		if [[ "$technology" == "quartz-seq2-384" ]]; then
		for convFile in "${convFiles[@]}"; do
		#remove adapter if detected
		@@ -1482,8 +1483,7 @@ else
		done
		fi


		#remove adapter from Sci-Seq and swap barcode and UMI
		#Sci-Seq: remove adapter and swap barcode and UMI
		if [[ "$technology" == "sciseq" ]]; then
		for convFile in "${convFiles[@]}"; do
		#remove adapter if detected
		@@ -1495,13 +1495,13 @@ else
		s/^(.{18})//g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		#swap UMI and barcode
		#swap barcode and UMI
		sed -E '2~2s/(.{8})(.{10})/\2\1/' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		fi

		#remove adapter from SureCell (and correct phase blocks)
		#SureCell: remove adapter and correct phase blocks
		if [[ "$technology" == "surecell" ]]; then
		for convFile in "${convFiles[@]}"; do
		#remove phase blocks and linkers
		@@ -1516,32 +1516,32 @@ else
		done
		fi

		# SPLiT-Seq can be set up similarly if a whitelist and 18bp barcode can be supported
		## https://github.com/hms-dbmi/dropEst/issues/80
		if [[ "$technology" == "surecell" ]]; then
		#SCRB-Seq: remove adapter
		if [[ "$technology" == "scrbseq" ]]; then
		for convFile in "${convFiles[@]}"; do
		#remove phase blocks and linkers (swap UMI and barcode)
		#remove adapters
		sed -E '
		/^([ATCGA]{92})/ {
		s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})*/\2\3\4\1/g
		/TCTTCCGATCT(.{6})(.{10})/ {
		s/TCTTCCGATCT(.{6})(.{10})/\1\2/g
		n
		n
		s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})*/\2\3\4\1/g
		s/.{11}(.{6})(.{10})/\1\2/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		fi

		#remove adapter from SCRB-Seq
		if [[ "$technology" == "scrbseq" ]]; then
		#SPLiT-Seq: correct phase blocks and swap barcode and UMI
		## https://github.com/hms-dbmi/dropEst/issues/80
		if [[ "$technology" == "surecell" ]]; then
		for convFile in "${convFiles[@]}"; do
		#remove adapters
		#remove phase blocks and linkers (swap barcode and UMI)
		sed -E '
		/TCTTCCGATCT(.{6})(.{10})/ {
		s/TCTTCCGATCT(.{6})(.{10})/\1\2/g
		/^([ATCGA]{92})/ {
		s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})*/\2\3\4\1/g
		n
		n
		s/.{11}(.{6})(.{10})/\1\2/g
		s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})*/\2\3\4\1/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done

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