Merge branch 'master' of dgt-gitlab.gsc.riken.jp:tom/cellranger_convert into dgt/kai (93dbe42e) · Commits · github_fork / Universc

CHANGELOG

0 → 100644

+40 −0

Original line number	Diff line number	Diff line

		### 0.2.2

		allow passing custom barcode whitelists

		### 0.2.1

		locate script directory

		implement lock file to prevent multi technologies running

		track last technology ran

		### 0.2.0

		add support for SGE mode

		correct passing description arguments to cellranger

		separate whitelist setup for Nadia and iCELL8

		configure cellranger version 3 whitelists

		add defaults

		detect lane and file names

		create directory for converted R1sq

		### 0.1.0

		pass arguments to script

		add set up call to configure whitelist when needed

		includes a manual and version call

		detects input file

		converts files if technology other than 10x
		No newline at end of file

README.md

+1 −1

Original line number	Diff line number	Diff line
		### UniverSC version 0.2.0
		### UniverSC version 0.2.2

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

launch_universc.sh

+95 −6

Original line number	Diff line number	Diff line
		@@ -62,6 +62,12 @@ Mandatory arguments to long options are mandatory for short options too.
		-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: 'SC3Pv2' (default), 'SC5P-PE', or 'SC5P-R2'
		-n, --force-cells NUM Force pipeline to use this number of cells, bypassing the cell detection algorithm.
		-j, --jobmode MODE Job manager to use. Valid options: 'local' (default), 'sge', 'lsf', or a .template file
		--localcores=NUM Set max cores the pipeline may request at one time.
		Only applies when --jobmode=local.
		--localmem=NUM Set max GB the pipeline may request at one time.
		Only applies when --jobmode=local.
		--mempercore=NUM Set max GB each job may use at one time.
		Only applies in cluster jobmodes.
		-p, --pass Skips the FASTQ file conversion if converted files already exist
		-h, --help Display this help and exit
		-v, --version Output version information and exit
		@@ -107,6 +113,8 @@ reference=""
		ncells=""
		chemistry=""
		jobmode=""
		ncores=""
		mem=""

		next=false
		for op in "$@"; do
		@@ -263,6 +271,39 @@ for op in "$@"; do
		exit 1
		fi
		;;
		--localcores)
		shift
		if [[ "$1" != "" ]]; then
		ncores="${1/%\//}"
		next=true
		shift
		else
		echo "Error: value missing for --localcores"
		exit 1
		fi
		;;
		--localmem)
		shift
		if [[ "$1" != "" ]]; then
		mem="${1/%\//}"
		next=true
		shift
		else
		echo "Error: value missing for --localmem"
		exit 1
		fi
		;;
		--mempercore)
		shift
		if [[ "$1" != "" ]]; then
		mem="${1/%\//}"
		next=true
		shift
		else
		echo "Error: value missing for --mempercore"
		exit 1
		fi
		;;
		-p\|--pass)
		convert=false
		next=false
		@@ -517,6 +558,23 @@ elif ! [[ $ncells =~ $int ]] && [[ $setup == "false" ]]; then
		echo "Error: option --force-cells must be an integer"
		exit 1
		fi
		#check if ncores is an integer
		int='^[0-9]+$'
		if [[ -z "$ncores" ]]; then
		ncores=""
		elif ! [[ $ncores =~ $int ]] && [[ $setup == "false" ]]; then
		echo "Error: option --localcores must be an integer"
		exit 1
		fi
		#check if mem is a number
		int='^[0-9]+([.][0-9]+)?$'
		if [[ -z "$mem" ]]; then
		mem=""
		elif ! [[ $mem =~ $int ]] && [[ $setup == "false" ]]; then
		echo "Error: option --localmem or --mempercore must be a number (of GB)"
		exit 1
		fi


		#check if chemistry matches expected input
		if [[ -z "$chemistry" ]]; then
		@@ -572,10 +630,12 @@ else
		echo "checking .lock file"
		lock=`cat $lockfile`

		if [[ $lock -eq 0 ]]; then
		if [[ $lock -le 0 ]]; then
		echo " call accepted: no other cellranger jobs running"
		lock=1
		if [[ $setup == false ]]; then
		echo $lock > $lockfile
		fi
		else
		if [[ -f $lastcallfile ]]; then
		echo " total of $lock cellranger ${VERSION} jobs already running in ${DIR} with technology $lastcall"
		@@ -590,7 +650,9 @@ else
		echo " call accepted: no conflict detected with other jobs currently running"
		#add current job to lock
		lock=$(($lock+1))
		if [[ $setup == false ]]; then
		echo $lock > $lockfile
		fi
		setup=false
		else
		echo "Error: conflict between technology selected for the new job ($technology) and other jobs currently running ($lastcall)"
		@@ -819,6 +881,7 @@ if [[ $setup == "true" ]]; then
		echo $technology > $lastcallfile
		fi
		cd -
		exit 0
		echo "setup complete"
		fi

		@@ -925,9 +988,31 @@ if [[ -n $ncells ]]; then
		n="--force-cells=$ncells"
		fi
		j=""
		l=""
		m=""
		if [[ -n $jobmode ]]; then
		j="--jobmode=$jobmode"
		if [[ $jobmode == "local" ]]; then
		if [[ -n $ncores ]]; then
		l="--localcores=$ncores"
		fi
		if [[ -n $mem ]]; then
		m="--localmem=$mem"
		fi
		else
		if [[ -n $mem ]]; then
		m="--mempercore=$mem"
		fi
		fi
		else
		if [[ -n $ncores ]]; then
		l="--localcores=$ncores"
		fi
		if [[ -n $mem ]]; then
		m="--localmem=$mem"
		fi
		fi

		start=`date +%s`
		echo "cellranger count --id=$id \
		--fastqs=$crIN \
		@@ -938,7 +1023,9 @@ echo "cellranger count --id=$id \
		--sample=$SAMPLE \
		$d \
		$n \
		$j
		$j \
		$l \
		$m
		"

		cellranger count --id=$id \
		@@ -950,7 +1037,9 @@ cellranger count --id=$id \
		--sample=$SAMPLE \
		$d \
		$n \
		$j
		$j \
		$l \
		$m
		# --noexit
		# --nopreflight
		end=`date +%s`

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