accept all inputs (30c546d2) · Commits · github_fork / Universc

crconverter_open.sh

+122 −12

Original line number	Diff line number	Diff line
		@@ -67,19 +67,19 @@ The code in this repository is licensed under the MIT License.
		#variable optionsname=false
		name=$1
		type=$2
		read1=()
		read2=()
		SAMPLE=""
		LANE=()
		id=""
		inpath=""
		output=""
		pipestance=""
		metrics=""
		analysis=""
		aggregation=""
		gemgroups=""
		contiginfo=""
		peaks=""
		fragmentsindex=""
		geneannotations=""
		geneannotationtypes=""
		description=""
		reference=""
		ncells=""
		chemistry="SC3Pv2"
		jobmode="local"
		ncores=""
		mem=""
		percelldata=false

		next=false
		end=false
		@@ -110,6 +110,116 @@ for op in "${@:3}"; do
		echo "Explicit setting of input using other flags will override inputs found with --inpath"
		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
		;;
		--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

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