sorted options (4bbe6cb9) · Commits · github_fork / Universc

launch_universc.sh

+52 −45

Original line number	Diff line number	Diff line
		@@ -18,7 +18,7 @@ cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2



		#####locate launch_universc.sh for importing barcodes######
		#####locate launch_universc.sh, barcode sources, and other tools######
		SOURCE="${BASH_SOURCE[0]}"
		SDIR=""
		RDIR=""
		@@ -50,28 +50,29 @@ PERCELLSTATS=${SDIR}/ExtractBasicStats.pl
		#####usage statement#####
		help='
		Usage:
		bash '$(basename $0)' --testrun -t THECHNOLOGY
		bash '$(basename $0)' -t TECHNOLOGY --setup
		bash '$(basename $0)' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
		bash '$(basename $0)' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
		bash '$(basename $0)' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
		bash '$(basename $0)' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
		bash '$(basename $0)' -v
		bash '$(basename $0)' -h
		bash '$(basename $0)' -t TECHNOLOGY --setup

		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.
		-t, --technology PLATFORM Name of technology used to generate data (10x, nadia, icell8, or custom)
		e.g. custom_16_10
		--testrun Initiates a test trun with the test dataset
		-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 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, --barcodefile FILE Custom 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.
		-t, --technology PLATFORM Name of technology used to generate data (10x, nadia, icell8, or custom)
		e.g. custom_16_10
		-b, --barcodefile FILE Custom barcode list in plain text

		-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.
		@@ -120,7 +121,8 @@ lastcall=`[ -e $lastcallfile ] && cat $lastcallfile \|\| echo ""`
		barcodedir=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes #folder within cellranger with the whitelist barcodes
		barcodefile=""
		crIN=input4cellranger #name of the directory with all FASTQ files given to cellranger
		percellfile="outs/basic_stats.txt"
		whitelistfile="outs/whitelist.txt" #name of the whitelist file added to the cellranger output
		percellfile="outs/basic_stats.txt" #name of the file with the basic statistics of the run added to the cellranger output

		#variable options
		setup=false
		@@ -147,37 +149,11 @@ for op in "$@"; do
		continue;
		fi
		case "$op" in
		-v\|--version)
		echo "launch_universc.sh version ${convertversion}"
		echo "cellranger version ${cellrangerversion}"
		exit 0
		;;
		-h\|--help)
		echo "$help"
		exit 0
		;;
		-s\|--setup)
		setup=true
		next=false
		shift
		;;
		--testrun)
		testrun=true
		next=false
		shift
		;;
		-t\|--technology)
		shift
		if [[ $1 != "" ]]; then
		technology="${1/%\//}"
		technology=`echo "$technology" \| tr '[:upper:]' '[:lower:]'`
		next=true
		shift
		else
		echo "Error: value missing for --technology"
		exit 1
		fi
		;;
		-R1\|--read1)
		shift
		if [[ "$1" != "" ]]; then
		@@ -224,17 +200,6 @@ for op in "$@"; do
		exit 1
		fi
		;;
		-b\|--barcodefile)
		shift
		if [[ "$1" != "" ]]; then
		barcodefile="${1/%\//}"
		next=true
		shift
		else
		echo "Error: value missing for --barcodefile"
		exit 1
		fi
		;;
		-i\|--id)
		shift
		if [[ "$1" != "" ]]; then
		@@ -268,6 +233,29 @@ for op in "$@"; do
		exit 1
		fi
		;;
		-t\|--technology)
		shift
		if [[ $1 != "" ]]; then
		technology="${1/%\//}"
		technology=`echo "$technology" \| tr '[:upper:]' '[:lower:]'`
		next=true
		shift
		else
		echo "Error: value missing for --technology"
		exit 1
		fi
		;;
		-b\|--barcodefile)
		shift
		if [[ "$1" != "" ]]; then
		barcodefile="${1/%\//}"
		next=true
		shift
		else
		echo "Error: value missing for --barcodefile"
		exit 1
		fi
		;;
		-c\|--chemistry)
		shift
		if [[ "$1" != "" ]]; then
		@@ -339,11 +327,25 @@ for op in "$@"; do
		next=false
		shift
		;;
		-s\|--setup)
		setup=true
		next=false
		shift
		;;
		-a\|--as-is)
		convert=false
		next=false
		shift
		;;
		-h\|--help)
		echo "$help"
		exit 0
		;;
		-v\|--version)
		echo "launch_universc.sh version ${convertversion}"
		echo "cellranger version ${cellrangerversion}"
		exit 0
		;;
		--verbose)
		echo "debugging mode activated"
		verbose=true
		@@ -367,6 +369,11 @@ fi

		#check if this is a test run
		if [[ $testrun == "true" ]]; then
		if [[ ]] \|\| [[ ]]; then
		echo "Error: for test run, no R1 or R2 file can be selected."
		exit 1
		fi

		reference=${SDIR}/test/cellranger_reference/cellranger-tiny-ref/3.0.0
		if [[ -z $id ]]; then
		id=test-tiny-${technology}

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