Merge branch 'master' of dgt-gitlab.gsc.riken.jp:tom/cellranger_convert (331f14cb) · Commits · github_fork / Universc

launch_universc.sh

+38 −11

Original line number	Diff line number	Diff line
		@@ -82,9 +82,10 @@ Mandatory arguments to long options are mandatory for short options too.
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq
		SeqWell (12bp barcode, 8bp UMI): seqwell
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq
		SCRUB-Seq (6bp barcode, 10bp UMI): scrubseq
		SureCell (18bp barcode, 8bp UMI): surecell, biorad
		SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10
		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)
		@@ -496,16 +497,20 @@ if [[ "$technology" == "sciseq" ]] \|\| [[ "$technology" == "sci-seq" ]]; then
		echo "Running with Sci-Seq parameters (single-cell combinatorial indexing RNA sequencing)"
		technology="sciseq"
		fi
		if [[ "$technology" == "scrubseq" ]] \|\| [[ "$technology" == "scrub-seq" ]]; then
		echo "Running with SCRUB-Seq parameters"
		technology="scrubseq"
		if [[ "$technology" == "scrbseq" ]] \|\| [[ "$technology" == "scrb-seq" ]] \|\| [[ "$technology" == "mcscrbseq" ]] \|\| [[ "$technology" == "mcscrb-seq" ]]; then
		echo "Running with SCRB-Seq / mcSCRB-seq parameters"
		technology="scrbseq"
		fi
		if [[ "$technology" == "seqwell" ]] \|\| [[ "$technology" == "seq-well" ]]; then
		echo "Running with Sci-Seq-Well parameters"
		technology="seqwell"
		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
		if [[ "$technology" == "surecell" ]] \|\| [[ "$technology" == "surecellseq" ]] \|\| [[ "$technology" == "surecell-seq" ]]\|\| [[ "$technology" == "bioraad" ]]; then
		if [[ "$technology" == "surecell" ]] \|\| [[ "$technology" == "surecellseq" ]] \|\| [[ "$technology" == "surecell-seq" ]] \|\| [[ "$technology" == "ddseq" ]] \|\| [[ "$technology" == "dd-seq" ]] \|\| [[ "$technology" == "bioraad" ]]; then
		echo "Running with SureCell parameters"
		technology="surecell"
		fi
		@@ -531,7 +536,8 @@ if [[ "$technology" != "10x" ]] \
		&& [[ "$technology" != "indrop"* ]] \
		&& [[ "$technology" != "quartz-seq2"* ]] \
		&& [[ "$technology" != "sciseq" ]] \
		&& [[ "$technology" != "scrubseq" ]] \
		&& [[ "$technology" != "scrbseq" ]] \
		&& [[ "$technology" != "seqwell" ]] \
		&& [[ "$technology" != "smart-seq"* ]]\
		&& [[ "$technology" != "surecell" ]]; then
		if [[ "$technology" != "custom"* ]]; then
		@@ -793,7 +799,7 @@ else
		echo "*WARNING: barcodes not available for Smart-Seq 2 or 3, using iCELL8 whitelist (version 3)*"
		echo "...valid barcodes may be an overestimate"
		barcodefile=${SDIR}/iCell8_barcode.txt
		elif [[ "$technology" == "custom"* ]] \|\| [[ "$technology" == "celseq"* ]] \|\| [[ "$technology" == "scrubseq" ]] \|\| [[ "$technology" == "sciseq" ]] \|\| [[ "$technology" == "surecell" ]]; then
		elif [[ "$technology" == "custom"* ]] \|\| [[ "$technology" == "celseq"* ]] \|\| [[ "$technology" == "sciseq" ]] \|\| [[ "$technology" == "scrbseq" ]] \|\| [[ "$technology" == "seqwell" ]] \|\| [[ "$technology" == "surecell" ]]; then
		if [[ "$technology" == "celseq" ]]; then
		customname="celseq"
		minlength=8
		@@ -803,9 +809,12 @@ else
		elif [[ "$technology" == "sciseq" ]]; then
		customname="sciseq"
		minlength=10
		elif [[ "$technology" == "scrubseq" ]]; then
		customname="scrubseq"
		elif [[ "$technology" == "scrbseq" ]]; then
		customname="scrbseq"
		minlength=6
		elif [[ "$technology" == "seqwell" ]]; then
		customname="seqwell"
		minlength=12
		elif [[ "$technology" == "surecell" ]]; then
		customname="surecell"
		barcodelength=18
		@@ -964,9 +973,12 @@ elif [[ "$technology" == "quartz-seq2-1536" ]]; then
		elif [[ "$technology" == "sciseq" ]]; then
		barcodelength=10
		umilength=8
		elif [[ "$technology" == "scrubseq" ]]; then
		elif [[ "$technology" == "scrbseq" ]]; then
		barcodelength=6
		umilength=10
		elif [[ "$technology" == "seqwell" ]]; then
		barcodelength=8
		umilength=12
		elif [[ "$technology" == "smartseq" ]]; then
		barcodelength=11
		umilength=8
		@@ -1313,6 +1325,21 @@ else
		done
		fi

		#remove adapter from SCRB-Seq
		if [[ "$technology" == "scrbseq" ]];
		for convFile in "${convFiles[@]}"; do
		#remove adapters
		sed -E '
		/TCTTCCGATCT(.{6})(.{10})/ {
		s/TCTTCCGATCT(.{6})(.{10})/\1\2/g
		n
		n
		s/.{11}(.{6})(.{10})/\1\2/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		fi

		#converting barcodes
		echo " adjusting barcodes of R1 files"
		if [[ $barcodeadjust != 0 ]]; then

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