Merge branch 'master' of dgt-gitlab.gsc.riken.jp:tom/cellranger_convert (6d8436ce) · Commits · github_fork / Universc

launch_universc.sh

+87 −3

Original line number	Original line	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'		-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.		-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		-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		-p, --pass Skips the FASTQ file conversion if converted files already exist
	-h, --help Display this help and exit		-h, --help Display this help and exit
	-v, --version Output version information and exit		-v, --version Output version information and exit
	@@ -107,6 +113,8 @@ reference=""
	ncells=""		ncells=""
	chemistry=""		chemistry=""
	jobmode=""		jobmode=""
			ncores=""
			mem=""

	next=false		next=false
	for op in "$@"; do		for op in "$@"; do
	@@ -263,6 +271,39 @@ for op in "$@"; do
	exit 1		exit 1
	fi		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)		-p\|--pass)
	convert=false		convert=false
	next=false		next=false
	@@ -517,6 +558,23 @@ elif ! [[ $ncells =~ $int ]] && [[ $setup == "false" ]]; then
	echo "Error: option --force-cells must be an integer"		echo "Error: option --force-cells must be an integer"
	exit 1		exit 1
	fi		fi
			#check if ncores is an integer
			ncores='^[0-9]+$'
			if [[ -z "$ncells" ]]; 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
			ncells=""
			elif ! [[ $ncells =~ $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		#check if chemistry matches expected input
	if [[ -z "$chemistry" ]]; then		if [[ -z "$chemistry" ]]; then
	@@ -925,9 +983,31 @@ if [[ -n $ncells ]]; then
	n="--force-cells=$ncells"		n="--force-cells=$ncells"
	fi		fi
	j=""		j=""
			l=""
			m=""
	if [[ -n $jobmode ]]; then		if [[ -n $jobmode ]]; then
	j="--jobmode=$jobmode"		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		fi
			else
			if [[ -n $ncores ]]; then
			l="--localcores=$ncores"
			fi
			if [[ -n $mem ]]; then
			m="--localmem=$mem"
			fi
			fi

	start=`date +%s`		start=`date +%s`
	echo "cellranger count --id=$id \		echo "cellranger count --id=$id \
	--fastqs=$crIN \		--fastqs=$crIN \
	@@ -938,7 +1018,9 @@ echo "cellranger count --id=$id \
	--sample=$SAMPLE \		--sample=$SAMPLE \
	$d \		$d \
	$n \		$n \
	$j		$j \
			$l \
			$m
	"		"

	cellranger count --id=$id \		cellranger count --id=$id \
	@@ -950,7 +1032,9 @@ cellranger count --id=$id \
	--sample=$SAMPLE \		--sample=$SAMPLE \
	$d \		$d \
	$n \		$n \
	$j		$j \
			$l \
			$m
	# --noexit		# --noexit
	# --nopreflight		# --nopreflight
	end=`date +%s`		end=`date +%s`

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