allowing custom technology and custom barcode file (in progress) (48504e16) · Commits · github_fork / Universc

launch_universc.sh

+211 −184

Original line number	Diff line number	Diff line
		@@ -2,13 +2,19 @@

		install=false

		#####cellrenger version#####
		cellrangerpass=`which cellranger`
		if [[ -z $cellrangerpass ]]; then
		######convert version#####
		convertversion="0.2.2"
		##########



		####cellrenger version#####
		cellrangerpath=`which cellranger` #location of cellranger
		if [[ -z $cellrangerpath ]]; then
		echo "cellranger command is not found."
		exit 1
		fi
		ver_info=`paste -d "\n" <(cellranger count --version) <(echo conversion script version 0.2.2) \| head -n 3 \| tail -n 2`
		cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -d"(" -f2 \| cut -d")" -f1` #get cellranger version
		##########


		@@ -51,11 +57,13 @@ Convert sequencing data (FASTQ) from Nadia or iCELL8 platforms for compatibility

		Mandatory arguments to long options are mandatory for short options too.
		-s, --setup Set up whitelists for compatibility with new technology
		-t, --technology PLATFORM Name of technology used to generate data (10x, nadia, icell8)
		-t, --technology PLATFORM Name of technology used to generate data (10x, nadia, icell8, or custom)
		e.g. custom_16_10
		-R1, --read1 FILE Read 1 FASTQ file to pass to cellranger (cell barcodes and umi)
		-R2, --read2 FILE Read 2 FASTQ file to pass to cellranger
		-f, --file NAME Name of FASTQ files to pass to cellranger (prefix before R1 or R2)
		-b, --barcodes FILE custom iCELL8 barcode list in plain text
		-f, --file NAME Path and the name of FASTQ files to pass to cellranger (prefix before R1 or R2)
		e.g. /path/to/files/Example_S1_L001
		-b, --barcodes FILE Custom iCELL8 barcode list in plain text
		-i, --id ID A unique run id, used to name output folder
		-d, --description TEXT Sample description to embed in output files.
		-r, --reference DIR Path of directory containing 10x-compatible reference.
		@@ -78,6 +86,10 @@ For each fastq file, follow the naming convention below:
		e.g. EXAMPLE_S1_L001_R1_001.fastq
		Example_S4_L002_R2_001.fastq.gz

		For custom barcode and umi length, follow the format below:
		custom_<barcode>_<UMI>
		e.g. custom_16_10 (which is the same as 10x)

		Files will be renamed if they do not follow this format. File extension will be detected automatically.
		'

		@@ -91,12 +103,10 @@ fi

		#####options#####
		#set options
		DIR=`which cellranger` #location of cellranger
		VERSION=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -d"(" -f2 \| cut -d")" -f1` #get cellranger version
		lockfile=${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock #path for .lock file
		lastcallfile=${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called #path for .last_called
		lastcall=`cat $lastcallfile`
		barcodefolder=${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes #folder with the barcodes
		lockfile=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.lock #path for .lock file
		lastcallfile=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.last_called #path for .last_called
		lastcall=`[ -e $lastcallfile ] && echo 1 \|\| echo ""`
		barcodefolder=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes #folder with the barcodes
		crIN=input4cellranger #name of the directory with all FASTQ files given to cellranger

		#variable options
		@@ -124,7 +134,8 @@ for op in "$@"; do
		fi
		case "$op" in
		-v\|--version)
		echo "$ver_info"
		echo "launch_universc.sh version ${convertversion}"
		echo "cellranger version ${cellrangerversion}"
		exit 0
		;;
		-h\|--help)
		@@ -190,7 +201,7 @@ for op in "$@"; do
		done
		skip=true
		else
		echo "Error: File input missing --file or --read1"
		echo "Error: file input missing for --file"
		exit 1
		fi
		;;
		@@ -330,11 +341,34 @@ if [[ $verbose == "true" ]]; then
		echo "checking options ..."
		fi

		#check if cellranger is writable
		if [[ ! -w $lockfile ]]; then
		echo "Error: Trying to run cellranger installed at ${cellrangerpath}"
		echo "launch_universc.sh can only run with cellranger installed locally"
		echo "Install cellranger in a directory with write permissions such as /home/`whoami`/local and export to the PATH"
		echo "The following versions of cellranger are found:"
		echo " `whereis cellranger`"
		exit 1
		fi

		#check if technology matches expected inputs
		if [[ "$technology" != "10x" ]] && [[ "$technology" != "nadia" ]] && [[ "$technology" != "icell8" ]]; then
		echo "Error: option -t needs to be 10x, nadia, or icell8"
		if [[ "$technology" != "custom"* ]]; then
		echo "Error: option -t needs to be 10x, nadia, icell8, or custom_<barcode>_<UMI>"
		exit 1
		else
		b=`echo $technology \| cut -f 2 -d'_'`
		u=`echo $technology \| cut -f 3 -d'_'`
		if ! [[ "$b" =~ ^[0-9]+$ ]] \|\| ! [[ "$u" =~ ^[0-9]+$ ]]; then
		echo "Error: option -t needs to be 10x, nadia, icell8, or custom_<barcode>_<UMI>"
		exit 1
		fi
		if [[ -z $barcodes ]]; then
		echo "Error: when -t is set as custom, a file with a list of barcodes needs to be specified."
		exit 1
		fi
		fi
		fi

		#check for presence of read1 and read2 files
		if [[ $setup == "false" ]]; then
		@@ -535,12 +569,10 @@ LANE=$(echo "${LANE[@]}" \| tr ' ' '\n' \| sort -u \| tr '\n' ',' \| sed 's/,$//')
		if [[ ! -z "$barcodes" ]]; then
		if [[ ! -f $barcodes ]]; then
		echo "Error: File selected for --barcode does not exist"
		elif [[ "$technology" != "icell8" ]]; then
		echo "Error: option --barcodes is only valid when --technology is icell8 yet its currently set as $technology."
		exit 1
		else
		barcodes=`readlink -f $barcodes`
		fi
		fi
		barcodes=`readlink -f $barcodes`

		#check if reference is present
		if [[ -z $reference ]]; then
		@@ -638,7 +670,7 @@ else
		fi
		else
		if [[ -f $lastcallfile ]]; then
		echo " total of $lock cellranger ${VERSION} jobs already running in ${DIR} with technology $lastcall"
		echo " total of $lock cellranger ${cellrangerversion} jobs already running in ${cellrangerpath} with technology $lastcall"

		#check if the technology running is different from the current convert call
		if [[ $lastcall == "icell8_custom" ]]; then
		@@ -729,54 +761,36 @@ echo ""
		#run setup if called
		if [[ $setup == "true" ]]; then
		echo "setup begin"
		echo "updating barcodes in $barcodefolder for cellranger version $VERSION installed in $DIR ..."

		if [[ ! -w $barcodefolder ]]; then
		echo "Error: launch_universc.sh can only be run cellranger installed locally"
		echo "Running cellranger installed at $DIR"
		echo "Install cellranger in a directory with write permissions such as /home/`whoami`/local"
		echo "cellranger must be exported to the PATH"
		echo "The following versions of cellranger are found:"
		echo " `whereis cellranger`"
		exit 1
		fi
		echo "updating barcodes in $barcodefolder for cellranger version ${cellrangerversion} installed in ${cellrangerpath} ..."

		cd $barcodefolder

		#compressing v3 whilelist
		#compressing v3 whilelist if present
		if [[ -f 3M-february-2018.txt ]]; then
		gzip -f 3M-february-2018.txt
		fi

		#restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8)
		if [[ -f nadia_barcode.txt ]] \|\| [[ -f iCell8_barcode.txt ]]; then
		#restore 10x barcodes if launch_universc.sh has already been run
		if [[ -f nadia_barcode.txt.gz ]] \|\| [[ -f iCell8_barcode.txt.gz ]] \|\| [[ -f custom_barcodes.txt.gz ]]; then
		echo " restoring 10x barcodes for version 2 kit ..."
		cp 737K-august-2016.txt.backup 737K-august-2016.txt
		fi
		echo " whitelist converted for 10x compatibility with version 2 kit."

		if [[ $technology == "10x" ]]; then
		#create version 3 files if version 3 whitelist available
		if [[ -f 3M-february-2018.txt.gz ]]; then
		#restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8)
		if [[ -f nadia_barcode.txt ]] \|\| [[ -f iCell8_barcode.txt ]]; then
		echo " restoring 10x barcodes for version 3 kit ..."
		cp 3M-february-2018.txt.backup.gz 3M-february-2018.txt.gz
		fi
		echo " whitelist converted for 10x compatibility with version 3 kit."
		fi
		echo " whitelist converted for 10x compatibility with version 2 kit and version 3 kit."

		if [[ $technology == "10x" ]]; then
		#if cellranger version is 3 or greater, restore assert functions
		if [[ `printf '%s\n' '$VERSION 3.0.0' \| sort -V \| head -n 1` != $VERSION ]]; then
		if [[ `printf '%s\n' '${cellrangerversion} 3.0.0' \| sort -V \| head -n 1` != ${cellrangerversion} ]]; then
		#restore functions if other technology run previously
		if [[ $lastcall != $technology ]]; then
		sed -i "s/#if gem_group == prev_gem_group/if gem_group == prev_gem_group/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/#assert barcode_idx >= prev_barcode_idx/assert barcode_idx >= prev_barcode_idx/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${DIR}-cs/${VERSION}/lib/python/cellranger/molecule_counter.py
		sed -i "s/#if gem_group == prev_gem_group/if gem_group == prev_gem_group/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/#assert barcode_idx >= prev_barcode_idx/assert barcode_idx >= prev_barcode_idx/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/molecule_counter.py
		fi
		echo " $DIR restored for $technology"
		echo " ${cellrangerpath} restored for $technology"
		else
		echo " $DIR ready for $technology"
		echo " ${cellrangerpath} ready for $technology"
		fi
		else
		#save original barcode file (if doesn't already exist)
		@@ -784,6 +798,10 @@ if [[ $setup == "true" ]]; then
		echo " backing up whitelist of version 2 kit ..."
		cp 737K-august-2016.txt 737K-august-2016.txt.backup
		fi
		if [[ -f 3M-february-2018.txt.gz ]] && [[ ! -f 3M-february-2018.txt.backup.gz ]]; then
		echo " backing up whitelist of version 3 kit ..."
		cp 3M-february-2018.txt.gz 3M-february-2018.txt.backup.gz
		fi

		#create a new version 2 barcode file
		if [[ $technology == "nadia" ]]; then
		@@ -792,99 +810,73 @@ if [[ $setup == "true" ]]; then
		if [[ -f nadia_barcide.txt.gz ]]; then
		gunzip -f nadia_barcode.txt.gz
		else
		echo AAAA{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G} \| sed 's/ /\n/g' > nadia_barcode.txt
		echo AAAA{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G} \| sed 's/ /\n/g' \| sort \| uniq > nadia_barcode.txt
		gzip -f nadia_barcode.txt
		fi
		fi
		cat nadia_barcode.txt \| sort \| uniq > 737K-august-2016.txt
		zcat nadia_barcode.txt.gz > 737K-august-2016.txt
		elif [[ $technology == "icell8" ]]; then
		#create an iCell8 barcode file by copying from convert repo
		if [[ -f iCell8_barcode.txt.gz ]]; then
		rm iCell8_barcode.txt.gz
		fi
		if [[ -f iCell8_barcode.txt ]]; then
		rm iCell8_barcode.txt
		fi

		if [[ -z $barcodes ]]; then
		cat ${SCRIPT_DIR}/iCell8_barcode.txt >$barcodefolder/iCell8_barcode.txt
		else
		cat $barcodes >$barcodefolder/iCell8_barcode.txt
		fi
		sed -i 's/^/AAAAA/g' iCell8_barcode.txt #convert barcode whitelist to match converted barcodes
		cat iCell8_barcode.txt \| sort \| uniq > 737K-august-2016.txt
		else
		lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`
		lock=$(($lock-1))
		echo $lock > $lockfile
		echo "Error: technology ($technology) is not supported"
		cd -
		exit 1
		sed -i 's/^/AAAAA/g' iCell8_barcode.txt \| sort \| uniq > iCell8_barcode.txt #convert barcode whitelist to match converted barcodes
		gzip -f iCell8_barcode.txt
		zcat iCell8_barcode.txt.gz > 737K-august-2016.txt
		fi
		if [[ $technology == "custom"* ]] \|\| [[ ! -z $barcodes ]]; then
		#create a custom barcode file by copying from selected barcode file
		cat ${barcodes} >$barcodefolder/custom_barcodes.txt
		barcodelength=`echo $technology \| cut -f 2 -d'_'`
		barcodeadjust=$(($barcodelength-16))
		if [[ $barcodeadjust -gt 0 ]]; then
		sed -i "s/^.{${barcodeadjust}}//" custom_barcodes.txt #Trim the first n characters from the beginning of the sequence and quality
		elif [[ 0 -gt $barcodeadjust ]]; then
		As=`printf '%0.sA' $(seq 1 $(($barcodeadjust * -1)))`
		sed -i "s/^/$As/" custom_barcodes.txt #Trim the first n characters from the beginning of the quality
		fi
		gzip -f custom_barcodes.txt
		zcat custom_barcodes.txt.gz > 737K-august-2016.txt
		fi
		echo " whitelist converted for $technology compatibility with version 2 kit."

		#create new version 3 files if version 3 whitelist available
		if [[ -f 3M-february-2018.txt.gz ]]; then
		#restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8)
		if [[ -f nadia_barcode.txt ]] \|\| [[ -f iCell8_barcode.txt ]]; then
		echo " restoring 10x barcodes for version 3 kit ..."
		cp 3M-february-2018.txt.backup.gz 3M-february-2018.txt.gz
		fi
		gunzip -k -f 3M-february-2018.txt.gz
		if [[ ! -f 3M-february-2018.txt.backup.gz ]]; then
		echo " backing up whitelist of version 3 kit ..."
		cp 3M-february-2018.txt 3M-february-2018.txt.backup
		gzip 3M-february-2018.txt.backup
		fi

		#combine 10x and new barcodes
		if [[ $technology == "nadia" ]]; then
		if [[ ! -f nadia_barcode.txt.gz ]]; then
		gzip -f nadia_barcode.txt
		fi
		zcat nadia_barcode.txt.gz 3M-february-2018.txt.backup.gz \| sort \| uniq > 3M-february-2018.txt
		elif [[ $technology == "icell8" ]]; then
		if [[ -f iCell8_barcode.txt.gz ]]; then
		rm iCell8_barcode.txt.gz
		fi
		if [[ -z $barcodes ]]; then
		cat ${SCRIPT_DIR}/iCell8_barcode.txt > 3M-february-2018.txt
		else
		cat ${barcodes} > 3M-february-2018.txt
		fi
		fi
		#create a new version 3 barcode file (if available)
		if [[ -f 3M-february-2018.txt.gz ]] && [[ -d translation ]]; then
		rm 3M-february-2018.txt.gz
		cp 737K-august-2016.txt 3M-february-2018.txt
		gzip -f 3M-february-2018.txt

		if [[ -d translation ]]; then
		rm translation/3M-february-2018.txt.gz
		ln -s ../3M-february-2018.txt.gz translation/3M-february-2018.txt.gz
		fi
		ln -s 3M-february-2018.txt.gz translation/3M-february-2018.txt.gz
		fi
		echo " whitelist converted for $technology compatibility with version 3 kit."

		#if cellranger version is 3 or greater, restore assert functions
		if [[ `printf '%s\n' '$VERSION 3.0.0' \| sort -V \| head -n 1` != $VERSION ]]; then
		if [[ `printf '%s\n' '${cellrangerversion} 3.0.0' \| sort -V \| head -n 1` != ${cellrangerversion} ]]; then
		#disable functions if 10x technology run previously
		if [[ $lastcall == "10x" ]]; then
		sed -i "s/if gem_group == prev_gem_group/#if gem_group == prev_gem_group/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/assert barcode_idx >= prev_barcode_idx/#assert barcode_idx >= prev_barcode_idx/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/assert np.array_equal(in_mc.get_barcodes(), barcodes)/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${DIR}-cs/${VERSION}/lib/python/cellranger/molecule_counter.py
		sed -i "s/if gem_group == prev_gem_group/#if gem_group == prev_gem_group/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/assert barcode_idx >= prev_barcode_idx/#assert barcode_idx >= prev_barcode_idx/g" ${cellrangerpath}-cs/${cellragerversion}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/assert np.array_equal(in_mc.get_barcodes(), barcodes)/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/molecule_counter.py
		fi
		echo " $DIR restored for $technology"
		echo " ${cellrangerpath} restored for $technology"
		else
		echo " $DIR ready for $technology"
		echo " ${cellrangerpath} ready for $technology"
		fi
		fi

		if [[ ! -z $barcodes ]]; then
		echo ${technology}_custom > $lastcallfile
		echo "custom" > $lastcallfile
		else
		echo $technology > $lastcallfile
		fi
		cd -
		exit 0

		cd - > /dev/null

		echo "setup complete"
		fi
		#########



		#####exiting when setup is all that is requested#####
		if [[ ${#read1[@]} -eq 0 ]] && [[ ${#read2[@]} -eq 0 ]]; then
		lock=`cat $lockfile`
		lock=$(($lock-1))
		@@ -944,41 +936,68 @@ done

		#####convert file format#####
		echo "converting input files to confer cellranger format ..."
		if [[ $convert = "false" ]]; then

		#determining the length for adjustment
		barcodelength=""
		umilength=""
		if [[ "$technology" == "10x" ]]; then
		barcodelength=16
		umilength=10
		elif [[ "$technology" == "nadia" ]]; then
		barcodelength=12
		umilength=8
		elif [[ "$technology" == "icell8" ]]; then
		barcodelength=11
		umilength=14
		else
		barcodelength=`echo $technology \| cut -f 2 -d'_'`
		umilength=`echo $technology \| cut -f 3 -d'_'`
		fi

		barcodeadjust=`echo $(($barcodelength-16))`
		umiadjust=`echo $(($umilength-12))`

		if [[ $convert == "false" ]]; then
		echo " input file format conversion skipped"
		fi

		if [[ "$technology" == "10x" ]]; then
		echo " 10x files accepted without conversion"
		elif [[ $convert == "true" ]]; then
		echo " converting file from $technology format to 10x format ..."
		#converting barcodes
		echo " adjusting barcodes of R1 files"
		if [[ $barcodeadjust != 0 ]] && [[ $convert == "true" ]]; then
		if [[ $barcodeadjust -gt 0 ]]; then
		for convFile in "${convFiles[@]}"; do
		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/' $convFile #Add quality scores for added bases
		echo " converting UMI"
		sed -i '2~4s/[NATCG][NATCG][NATCG][NATCG][NATCG][NATCG]$/AA/' $convFile #Replace last 6 bases with AA
		echo " converting quality scores"
		sed -i '4~4s/......$/II/' $convFile #Replace quality scores for added bases
		elif [[ "$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/' $convFile #Add quality scores for added bases
		sed -i "2~2s/^.{${barcodeadjust}}//" $convFile #Trim the first n characters from the beginning of the sequence and quality
		echo " ${convFile} adjusted"
		done
		elif [[ 0 -gt $barcodeadjust ]]; then
		for convFile in "${convFiles[@]}"; do
		toS=`printf '%0.sA' $(seq 1 $(($barcodeadjust * -1)))`
		toQ=`printf '%0.sI' $(seq 1 $(($barcodeadjust * -1)))`
		sed -i "2~4s/^/$toS/" $convFile #Trim the first n characters from the beginning of the sequence
		sed -i "4~4s/^/$toQ/" $convFile #Trim the first n characters from the beginning of the quality
		echo " ${convFile} adjusted"
		done
		fi
		fi
		#UMI
		echo " adjusting UMIs of R1 files"
		if [[ 0 -gt $umiadjust ]]; then
		for convFile in "${convFiles[@]}"; do
		toS=`printf '%0.sA' $(seq 1 $(($umiadjust * -1)))`
		toQ=`printf '%0.sI' $(seq 1 $(($umiadjust * -1)))`
		keeplength=`echo $((26-($umiadjust * -1)))`
		sed -i "2~2s/^$.\{${keeplength}\}$.*/\1/" $convFile #Trim off everything beyond what is needed
		sed -i "2~4s/$/$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
		echo " ${convFile} adjusted"
		done
		fi
		##########



		#####run cellranger#####
		echo "running cellranger ..."
		echo ""
		echo "#####cellranger#####"
		####run cellranger#####
		#setting opitons for cellranger
		d=""
		if [[ -n $description ]]; then
		d="--description=$description"
		@@ -1013,6 +1032,11 @@ else
		fi
		fi

		#outputting command
		echo "running cellranger ..."
		echo ""
		echo "#####cellranger#####"

		start=`date +%s`
		echo "cellranger count --id=$id \
		--fastqs=$crIN \
		@@ -1028,6 +1052,7 @@ echo "cellranger count --id=$id \
		$m
		"

		#running cellranger
		cellranger count --id=$id \
		--fastqs=$crIN \
		--lanes=$LANE \
		@@ -1042,6 +1067,8 @@ cellranger count --id=$id \
		$m
		# --noexit
		# --nopreflight

		#outputting log
		end=`date +%s`
		runtime=$((end-start))
		echo "##########"
		@@ -1054,14 +1081,14 @@ echo ""
		echo "updating .lock file"

		#remove currewnt job from counter (successfully completed)
		lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`
		lock=`cat ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.lock`
		lock=$(($lock-1))

		#check if jobs running
		if [[ $lock -ge 1 ]]; then
		echo " total of $lock jobs for $lastcall technology are still run by cellranger ${VERSION} in ${DIR}"
		echo " total of $lock jobs for $lastcall technology are still run by cellranger ${cellrangerversion} in ${cellrangerpath}"
		else
		echo " no other jobs currently run by cellranger ${VERSION} in ${DIR}"
		echo " no other jobs currently run by cellranger ${cellrangerversion} in ${cellrangerpath}"
		echo " no conflicts: whitelist can now be changed for other technologies"
		rm -f $lockfile
		fi
		@@ -1072,7 +1099,7 @@ fi
		#####printing out log#####
		log="
		#####Conversion tool log#####
		$ver_info
		cellranger ${cellrangerversion}

		Original barcode format: ${technology} (then converted to 10x)

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