support other technology aliases (c9016a63) · Commits · github_fork / Universc

launch_universc.sh

+13 −2

Original line number	Diff line number	Diff line
		@@ -69,7 +69,7 @@ Mandatory arguments to long options are mandatory for short options too.
		-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)
		-t, --technology PLATFORM Name of technology used to generate data (10x, chromium, nadia, dropseq, icell8, or custom)
		e.g. custom_16_10
		-b, --barcodefile FILE Custom barcode list in plain text

		@@ -418,6 +418,17 @@ if ! [[ -w "$SDIR" ]]; then
		exit 1
		fi


		#aliases for technology with the same settings
		if [[ "$technology" == "chromium" ]]; then
		echo "Running with technology 10x (chromium)"
		technology="10x"
		fi
		if [[ "$technology" == "dropseq" ]] \|\| [[ "$technology" == "drop-seq" ]]; then
		echo "Running with Nadia parameters (Drop-Seq)"
		technology="nadia"
		fi

		#check if technology matches expected inputs
		if [[ "$technology" != "10x" ]] && [[ "$technology" != "nadia" ]] && [[ "$technology" != "icell8" ]]; then
		if [[ "$technology" != "custom"* ]]; then
		@@ -648,7 +659,7 @@ if [[ ! -z "$barcodefile" ]]; then
		fi
		else
		if [[ "$technology" == "10x" ]]; then
		barcodefile=default
		barcodefile="default"
		elif [[ "$technology" == "nadia" ]]; then
		barcodefile=${SDIR}/nadia_barcode.txt
		if [[ ! -f ${barcodefile} ]]; then