Merge branch 'master' of dgt-gitlab.gsc.riken.jp:tom/cellranger_convert (940399a4) · Commits · github_fork / Universc

launch_universc.sh

+10 −11

Original line number	Diff line number	Diff line
		@@ -886,7 +886,7 @@ 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
		@@ -929,6 +929,7 @@ 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
		@@ -942,6 +943,7 @@ 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
		@@ -1297,21 +1299,18 @@ else
		done
		fi

		#remove adapter from Sci-Seq and swap barcode and UMI
		if [[ "$technology" == "sciseq" ]]; then
		#remove adapter from SureCell (and correct phase blocks)
		if [[ "$technology" == "surecell" ]]; then
		for convFile in "${convFiles[@]}"; do
		#remove adapter if detected
		#remove phase blocks and linkers
		sed -E '
		/^ACGACGCTCTTCCGATCT/ {
		s/^(.{18})//g
		/.*(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC/ {
		s/.(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC./\1\2\3\4/g
		n
		n
		s/^(.{18})//g
		s/.*(.{6}).{15}(.{6}).{15}(.{6}).{3}(.{8}).{3}/\1\2\3\4/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		#swap UMI and barcode
		sed -E '2~2s/(.{8})(.{10})/\2\1/' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		fi

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