Merge branch 'dev' of dgt-gitlab.gsc.riken.jp:tom/cellranger_convert into kai (014402dc) · Commits · github_fork / Universc

.gitignore

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			test/internal
			test-*

CHANGELOG

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			### 0.3.0 (in development)

			- custom whitelists for other technologies

			- configure custom input technology (kai)

			- test data for checking technologies (tom)

			- bundle as docker with cellranger for install (w.i.p.)

			- configure automated tested for GitLab or Travis CI

	### 0.2.2		### 0.2.2

	allow passing custom barcode whitelists		allow passing custom barcode whitelists (can only run in serial)

	### 0.2.1		### 0.2.1

README.md

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	### UniverSC version 0.2.2		### UniverSC version 0.3.0

	Conversion script to run Nadia and iCELL8 libraries with cellranger (10x Genomics analysis tool)		Conversion script to run Nadia, iCELL8, and custom libraries with cellranger (10x Genomics analysis tool)

	#### Tom Kelly (RIKEN IMS) and Kai Battenberg (RIKEN CSRS/IMS)		#### Tom Kelly (RIKEN IMS) and Kai Battenberg (RIKEN CSRS/IMS)

launch_universc.sh

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	@@ -3,7 +3,7 @@
	install=false		install=false

	######convert version#####		######convert version#####
	convertversion="0.2.4"		convertversion="0.3.0.9001"
	##########		##########


	@@ -14,7 +14,7 @@ if [[ -z $cellrangerpath ]]; then
	echo "cellranger command is not found."		echo "cellranger command is not found."
	exit 1		exit 1
	fi		fi
	cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -d"(" -f2 \| cut -d")" -f1` #get cellranger version		ver_info=`paste -d "\n" <(cellranger count --version) <(echo conversion script version 0.3.0.9001) \| head -n 3 \| tail -n 2`
	##########		##########


	@@ -984,6 +984,7 @@ fi
	echo " adjusting UMIs of R1 files"		echo " adjusting UMIs of R1 files"
	if [[ 0 -gt $umiadjust ]]; then		if [[ 0 -gt $umiadjust ]]; then
	for convFile in "${convFiles[@]}"; do		for convFile in "${convFiles[@]}"; do
			<<<<<<< HEAD
	toS=`printf '%0.sA' $(seq 1 $(($umiadjust * -1)))`		toS=`printf '%0.sA' $(seq 1 $(($umiadjust * -1)))`
	toQ=`printf '%0.sI' $(seq 1 $(($umiadjust * -1)))`		toQ=`printf '%0.sI' $(seq 1 $(($umiadjust * -1)))`
	keeplength=`echo $((${barcode_default}+${umi_default}-($umiadjust * -1)))`		keeplength=`echo $((${barcode_default}+${umi_default}-($umiadjust * -1)))`
	@@ -991,6 +992,24 @@ if [[ 0 -gt $umiadjust ]]; then
	sed -i "2~4s/$/$toS/" $convFile #Add n characters to the end of the sequence		sed -i "2~4s/$/$toS/" $convFile #Add n characters to the end of the sequence
	sed -i "4~4s/$/$toQ/" $convFile #Add n characters to the end of the quality		sed -i "4~4s/$/$toQ/" $convFile #Add n characters to the end of the quality
	echo " ${convFile} adjusted"		echo " ${convFile} adjusted"
			=======
			echo " handling $convFile ..."
			if [[ "$technology" == "nadia" ]]; then
			echo " converting barcodes"
			sed -i '2~4s/^/AAAA/' $convFile #Add AAAA to every read
			echo " converting quality scores"
			sed -i '4~4s/^/IIII/' $convFile #Add quality scores for added bases
			echo " converting UMI"
			sed -i '2~4s/[NATCG][NATCG][NATCG][NATCG]$//' $convFile #Remove last 4 bases
			echo " converting quality scores"
			sed -i '4~4s/....$//' $convFile #Replace quality scores for last 4 bases
			elif [[ "$technology" == "icell8" ]]; then
			echo " converting barcodes"
			sed -i '2~4s/^/AAAAA/' $convFile #Add AAAAA to every read
			echo " converting quality scores"
			sed -i '4~4s/^/IIIII/' $convFile #Add quality scores for added bases
			fi
			>>>>>>> e05b998d17d2c79ec3eec9784858acde747671ae
	done		done
	fi		fi
	##########		##########

test/shared/cellranger-tiny-fastq/1.2.0/.version

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			1.2.0
			No newline at end of file

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