allows custom barcode file for icell8 run (5ac143c3) · Commits · github_fork / Universc

launch_universc.sh

+77 −29

Original line number	Diff line number	Diff line
		@@ -47,7 +47,7 @@ Usage:
		bash '$(basename $0)' -h
		bash '$(basename $0)' -t TECHNOLOGY --setup

		Convert sequencing data (FASTQ) from various platforms for compatibility with 10x Genomics and run cellranger count
		Convert sequencing data (FASTQ) from Nadia or iCELL8 platforms for compatibility with 10x Genomics and run cellranger count

		Mandatory arguments to long options are mandatory for short options too.
		-s, --setup Set up whitelists for compatibility with new technology
		@@ -55,6 +55,7 @@ Mandatory arguments to long options are mandatory for short options too.
		-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
		-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.
		@@ -97,6 +98,7 @@ setup=false
		convert=true
		read1=()
		read2=()
		barcodes=""
		SAMPLE=""
		LANE=()
		id=""
		@@ -184,6 +186,17 @@ for op in "$@"; do
		exit 1
		fi
		;;
		-b\|--barcodes)
		shift
		if [[ "$1" != "" ]]; then
		barcodes="${1/%\//}"
		next=true
		shift
		else
		echo "Error: value missing for --barcodes"
		exit 1
		fi
		;;
		-i\|--id)
		shift
		if [[ "$1" != "" ]]; then
		@@ -321,7 +334,7 @@ for i in {1..2}; do
		fi
		elif [[ -f $read ]]; then
		if [[ $read == *"gz" ]]; then
		gunzip -k $read
		gunzip -f -k $read
		#update file variable
		read=`echo $read \| sed -e "s/\.gz//g"`
		fi
		@@ -330,14 +343,14 @@ for i in {1..2}; do
		exit 1
		fi
		#allow detection of file extension (needed for --file input)
		elif [ -f ${read}.fq ] \|\| [ -h ${read}.fq ]; then
		elif [[ -f ${read}.fq ]] \|\| [[ -h ${read}.fq ]]; then
		read=${read}.fq
		elif [ -f ${read}.fastq ] \|\| [ -h ${read}.fastq ]; then
		elif [[ -f ${read}.fastq ]] \|\| [[ -h ${read}.fastq ]]; then
		read=${read}.fastq
		elif [ -f ${read}.fq.gz ] \|\| [ -h ${read}.fq.gz ]; then
		elif [[ -f ${read}.fq.gz ]] \|\| [[ -h ${read}.fq.gz ]]; then
		gunzip -f -k ${read}.fq.gz
		read=${read}.fq
		elif [ -f ${read}.fastq.gz ] \|\| [ -h ${read}.fastq.gz ]; then
		elif [[ -f ${read}.fastq.gz ]] \|\| [[ -h ${read}.fastq.gz ]]; then
		gunzip -f -k ${read}.fastq.gz
		read=${read}.fastq
		else
		@@ -477,6 +490,17 @@ for fq in "${read12[@]}"; do
		done
		LANE=$(echo "${LANE[@]}" \| tr ' ' '\n' \| sort -u \| tr '\n' ',' \| sed 's/,$//')

		#checking the quality of custom barcode file
		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
		fi
		fi
		barcodes=`readlink -f $barcodes`

		#check if reference is present
		if [[ -z $reference ]]; then
		if [[ $setup == "false" ]] \|\| [[ ${#read1[@]} -ne 0 ]] \|\| [[ ${#read2[@]} -ne 0 ]]; then
		@@ -487,7 +511,7 @@ fi

		#check if ncells is an integer
		int='^[0-9]+$'
		if [ -z "$ncells" ]; then
		if [[ -z "$ncells" ]]; then
		ncells=""
		elif ! [[ $ncells =~ $int ]] && [[ $setup == "false" ]]; then
		echo "Error: option --force-cells must be an integer"
		@@ -495,7 +519,7 @@ elif ! [[ $ncells =~ $int ]] && [[ $setup == "false" ]]; then
		fi

		#check if chemistry matches expected input
		if [ -z "$chemistry" ]; then
		if [[ -z "$chemistry" ]]; then
		chemistry="SC3Pv2"
		elif [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then
		echo "Error: option --chemistry must be SC3Pv2, SC5P-PE , or SC5P-R2"
		@@ -503,7 +527,7 @@ elif [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$c
		fi

		#checking if jobmode matches expected input
		if [ -z "$jobmode" ]; then
		if [[ -z "$jobmode" ]]; then
		jobmode="local"
		elif [[ "$jobmode" != "local" ]] && [[ "$jobmode" != "sge" ]] && [[ "$jobmode" != "lsf" ]] && [[ "$jobmode" != *"template" ]]; then
		echo "Error: option --jobmode must be local, sge, lsf, or a .template file"
		@@ -530,7 +554,7 @@ if [[ -z $id ]]; then
		exit 1
		fi
		fi
		crIN=${crIN}_$id
		crIN=${crIN}_${id}
		if [[ ! -d ${crIN} ]]; then
		convert=true
		fi
		@@ -557,11 +581,17 @@ else
		echo " total of $lock cellranger ${VERSION} jobs already running in ${DIR} with technology $lastcall"

		#check if the technology running is different from the current convert call
		if [[ $lastcall == $technology ]]; then
		if [[ $lastcall == "icell8_custom" ]]; then
		echo "Error: icell8 with custom barcode list is currently running"
		echo "other jobs cannot be run until the current job is complete"
		echo "remove $lockfile if $lastcall jobs have completed or aborted"
		exit 1
		elif [[ $lastcall == $technology ]]; then
		echo " call accepted: no conflict detected with other jobs currently running"
		#add current job to lock
		lock=$(($lock+1))
		echo $lock > $lockfile
		setup=false
		else
		echo "Error: conflict between technology selected for the new job ($technology) and other jobs currently running ($lastcall)"
		echo "barcode whitelist configured and locked for currently running technology: $lastcall"
		@@ -585,6 +615,11 @@ echo "FORMAT: $technology"
		if [[ $technology == "nadia" ]]; then
		echo "*Warning: whitelist is converted for compatibility with $technology, valid barcodes cannot be detected accurately with this technology*"
		fi
		if [[ -z $barcodes ]]; then
		echo "BARCODES: default"
		else
		echo "BARCODES: (custom barcode file) $barcodes"
		fi
		if [[ ${#read1[@]} -eq 0 ]] && [[ ${#read1[@]} -eq 0 ]]; then
		echo "*Warning: no FASTQ files were selected, launch_universc.sh will exit after setting up the whitelist*"
		fi
		@@ -693,12 +728,12 @@ if [[ $setup == "true" ]]; then
		#create a Nadia barcode file
		if [[ ! -f nadia_barcode.txt ]]; then
		if [[ -f nadia_barcide.txt.gz ]]; then
		gunzip nadia_barcode.txt.gz
		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
		fi
		fi
		cat nadia_barcode.txt 737K-august-2016.txt.backup \| sort \| uniq > 737K-august-2016.txt
		cat nadia_barcode.txt \| sort \| uniq > 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
		@@ -707,9 +742,14 @@ if [[ $setup == "true" ]]; then
		if [[ -f iCell8_barcode.txt ]]; then
		rm iCell8_barcode.txt
		fi
		rsync -u ${SCRIPT_DIR}/iCell8_barcode.txt $barcodefolder/iCell8_barcode.txt

		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 737K-august-2016.txt.backup \| sort \| uniq > 737K-august-2016.txt
		cat iCell8_barcode.txt \| sort \| uniq > 737K-august-2016.txt
		else
		lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`
		lock=$(($lock-1))
		@@ -744,11 +784,15 @@ if [[ $setup == "true" ]]; then
		if [[ -f iCell8_barcode.txt.gz ]]; then
		rm iCell8_barcode.txt.gz
		fi
		cat iCell8_barcode.txt > 3M-february-2018.txt
		if [[ -z $barcodes ]]; then
		cat ${SCRIPT_DIR}/iCell8_barcode.txt > 3M-february-2018.txt
		else
		cat ${barcodes} > 3M-february-2018.txt
		fi
		fi
		gzip -f 3M-february-2018.txt

		if [ -d translation ]; then
		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
		@@ -769,7 +813,11 @@ if [[ $setup == "true" ]]; then
		fi
		fi

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

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