correct test jobs with cellranger calls (4787712b) · Commits · github_fork / Universc

.github/workflows/docker-test-call.yml

+4 −4

Original line number	Diff line number	Diff line
		@@ -38,7 +38,7 @@ jobs:
		- name: Diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/cellranger_clean:latest pwd;ls
		- name: Cell Ranger Call
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/cellranger_clean:latest cellranger -v
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/cellranger_clean:latest cellranger count --help

		test-repo:
		runs-on: ubuntu-latest
		@@ -49,9 +49,9 @@ jobs:
		- name: Where am i
		run: pwd; ls
		- name: pull updates
		run: cd universc; git pull origin master
		run: git pull origin master
		- name: call UniverSC
		run: ls /universc/launch_universc.sh
		run: ls launch_universc.sh

		test-universc:
		runs-on: ubuntu-20.04
		@@ -75,7 +75,7 @@ jobs:
		- name: Diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls
		- name: Cell Ranger Call
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest cellranger -v
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest cellranger count --help
		- name: UniverSC Call
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/launch_universc.sh -v
		- name: Run test calls

crconverter_open.sh

deleted100755 → 0

+0 −320

Original line number	Diff line number	Diff line
		#!/bin/bash


		######convert version#####
		crconverterversion="3.1.1.90001"
		##########



		#####cellranger version#####
		cellrangerpath=`which cellranger` #location of Cell Ranger
		if [[ -z $cellrangerpath ]]; then
		echo "cellranger command is not found."
		exit 1
		fi
		cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2 -d'(' \| cut -f1 -d')'`
		##########



		#####declare variables#####
		SOURCE="${BASH_SOURCE[0]}"
		##########



		#####usage statement#####
		statement='crconverter

		Usage:

		crconverter <name> <type> [options]
		crconverter -h \| --help \| --version
		'
		options='

		Options:
		--inpath=PATH Path to a completed pipestance. crconvert will attempt find inputs automatically by filename
		Explicit setting of input using other flags will override inputs found with --inpath
		--output=PATH
		--pipestance=PATH
		--metrics=PATH
		--analysis=PATH
		--matrix=PATH
		--aggregation=PATH
		--gemgroups=PATH
		--contiginfo=PATH
		--peaks=PATH
		--fragmentsindex=PATH
		--geneannotations=PATH
		--geneannotationtypes=TYPES
		--description=DESC
		-h --help
		--version

		This is an open-source implementation of crconverter.
		This is only intended for testing open-source implementations
		of Cell Ranger and may not produce the same results as
		software produced by 10x Genomics. We recommend the
		supported software be used for other purposes.

		The code in this repository is licensed under the MIT License.
		'
		##########




		#####print usage#####
		if [[ -z $1 ]]; then
		echo "$statement"
		exit 1
		fi
		##########




		#####declare variables#####
		name=$1
		type=$2
		inpath=""
		output=""
		pipestance=""
		metrics=""
		analysis=""
		matrix=""
		aggregation=""
		gemgroups=""
		contiginfo=""
		peaks=""
		fragmentsindex=""
		geneannotations=""
		geneannotationtypes=""
		description=""

		next=false
		end=false

		if [[ $1 == "-h" ]] \|\| [[ $2 == "-h" ]] \|\| [[ $1 == "--help" ]] \|\| [[ $2 == "--help" ]]; then
		end=true
		usage=true
		help=true
		fi

		if [[ $1 == "-v" ]] \|\| [[ $2 == "-v" ]] \|\| [[ $1 == "--version" ]] \|\| [[ $2 == "--version" ]]; then
		end=true
		version=true
		fi
		shift
		shift
		for op in "${@}"; do
		if $next; then
		next=false;
		continue;
		fi
		case "$op" in
		--inpath)
		shift
		if [[ "$1" != "" ]]; then
		inpath="${1/%\//}"
		next=true
		shift
		else
		echo "Explicit setting of input using other flags will override inputs found with --inpath"
		shift
		fi
		;;
		--output)
		shift
		if [[ "$1" != "" ]]; then
		output="${1/%\//}"
		next=true
		shift
		else
		output=""
		fi
		;;
		--pipestance)
		shift
		if [[ "$1" != "" ]]; then
		pipestance="${1/%\//}"
		next=true
		shift
		else
		pipestance=""
		fi
		;;
		--metrics)
		shift
		if [[ "$1" != "" ]]; then
		metrics="${1/%\//}"
		next=true
		shift
		else
		metrics=""
		fi
		;;
		--analysis)
		shift
		if [[ "$1" != "" ]]; then
		analysis="${1/%\//}"
		next=true
		shift
		else
		analysis=""
		fi
		;;
		--matrix)
		shift
		if [[ "$1" != "" ]]; then
		matrix="${1/%\//}"
		next=true
		shift
		else
		matrix=""
		fi
		;;
		--aggregation)
		shift
		if [[ "$1" != "" ]]; then
		aggregation="${1/%\//}"
		next=true
		shift
		else
		aggregation=""
		fi
		;;
		--gemgroups)
		shift
		if [[ "$1" != "" ]]; then
		gemgroups="${1/%\//}"
		next=true
		shift
		else
		gemgroups=""
		fi
		;;
		--contiginfo)
		shift
		if [[ "$1" != "" ]]; then
		contiginfo="${1/%\//}"
		next=true
		shift
		else
		contiginfo=""
		fi
		;;
		--peaks)
		shift
		if [[ "$1" != "" ]]; then
		peaks="${1/%\//}"
		next=true
		shift
		else
		peaks=""
		fi
		;;
		--fragmentsindex)
		shift
		if [[ "$1" != "" ]]; then
		fragmentsindex="${1/%\//}"
		next=true
		shift
		else
		fragmentsindex=""
		fi
		;;
		--geneannotations)
		shift
		if [[ "$1" != "" ]]; then
		geneannotations="${1/%\//}"
		next=true
		shift
		else
		geneannotations=""
		fi
		;;
		--geneannotationtypes)
		shift
		if [[ "$1" != "" ]]; then
		geneannotationtypes="${1/%\//}"
		next=true
		shift
		else
		geneannotationtypes=""
		fi
		;;
		--description)
		shift
		if [[ "$1" != "" ]]; then
		description="${1/%\//}"
		next=true
		shift
		else
		description=""
		fi
		;;
		-v\|--version)
		end=true
		version=true
		echo "$crconverterversion"
		exit 0
		;;
		-h\|--help)
		end=true
		usage=true
		help=true
		echo "$statement"
		echo "$options"
		exit 0
		;;
		--verbose)
		echo "debugging mode activated"
		verbose=true
		next=false
		shift
		;;
		-*)
		echo "Error: Invalid option: $op"
		exit 1
		;;
		esac
		done
		##########

		if [[ $end ]]; then
		if [[ ! -z $help ]]; then
		echo "$statement"
		echo "$options"
		exit 0
		fi
		fi

		if [[ $end ]]; then
		if [[ ! -z $version ]]; then
		echo "$crconverterversion"
		exit 0
		fi
		fi

		##########

		if [[ -z $output ]]; then
		echo "An output file must be specified"
		exit 1
		fi

		if [[ ! -f $output ]]; then
		echo "#!/bin/bash" > $output
		echo "echo \"Please use the supported release of Cell Ranger if you wish to use .cloupe files\"" >> $output
		chmod 755 $output
		else
		echo ".cloupe file already exists in $output"
		fi

		echo "Wrote .cloupe file to $output"
		echo "Warning .cloupe file may be dysfunctional"
		exit 0

run_cellranger.sh

deleted100644 → 0

+0 −50

Original line number	Diff line number	Diff line
		#!/bin/bash
		#$ -N cellranger_NPO1
		#$ -q bigmem.q
		#$ -o cellranger_NP01.out
		#$ -e cellranger_NP01_error.out
		#$ -cwd

		#create virtual directory of modified files
		if [ ! -d cellranger ]
		then
		mkdir -p cellranger
		fi
		for file in `ls R2.fastq \| cut -d"_" -f1-3`
		do
		if [ ! -f cellranger/${file}_R1_001.fastq ]
		then
		#ln -s ../${file}_cellranger_R1_001.fastq cellranger/${file}_R1_001.fastq
		ln -s ../${file}_cellranger_R1_001.fastq cellranger/${file}_R1_001.fastq
		fi
		if [ ! -f cellranger/${file}_R2_001.fastq ]
		then
		ln -s ../${file}_R2_001.fastq cellranger/${file}_R2_001.fastq
		fi
		done

		export PATH=/home/tom/local/bin/cellranger-2.1.0:$PATH

		date
		start=`date +%s`
		cellranger count --id="test_AtRTD2" \
		--fastqs="cellranger" \
		--sample="NP01" \
		--lanes="1,2" \
		--r1-length="26" \
		--chemistry="threeprime" \
		--transcriptome="/home/tom/reference/cellranger/AtRTDv2/"

		# --noexit \
		# --nopreflight

		# --force-cells="2500" \
		end=`date +%s`
		date

		runtime=$((end-start))

		#edit html output
		sed -i "s/test_AtRTD2/Arabidopsis $NP01$/g" test_AtRTD2/outs/web_summary.html
		sed -i "1621s/.*/ <td><i>Arabidopsis thaliana<\/i> (NP01)<\/td>/" test_AtRTD2/outs/web_summary.html

Admin message