enable running cellranger version 3 on converted whitelists (9844bfe8) · Commits · github_fork / Universc

launch_universc.sh

+5 −2

Original line number	Diff line number	Diff line
		@@ -764,6 +764,7 @@ if [[ $setup == "true" ]]; then
		if [[ `printf '%s\n' '$VERSION 3.0.0' \| sort -V \| head -n 1` != $VERSION ]]; then
		#restore functions if other technology run previously
		if [[ $lastcall != $technology ]]; then
		sed -i "s/#if gem_group == prev_gem_group/if gem_group == prev_gem_group/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/#assert barcode_idx >= prev_barcode_idx/assert barcode_idx >= prev_barcode_idx/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${DIR}-cs/${VERSION}/lib/python/cellranger/molecule_counter.py
		fi
		@@ -823,7 +824,8 @@ if [[ $setup == "true" ]]; then
		#if cellranger version is 3 or greater, restore assert functions
		if [[ `printf '%s\n' '$VERSION 3.0.0' \| sort -V \| head -n 1` != $VERSION ]]; then
		#disable functions if 10x technology run previously
		if [[ $lastcall != "10x" ]]; then
		if [[ $lastcall == "10x" ]]; then
		sed -i "s/if gem_group == prev_gem_group/#if gem_group == prev_gem_group/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/assert barcode_idx >= prev_barcode_idx/#assert barcode_idx >= prev_barcode_idx/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/assert np.array_equal(in_mc.get_barcodes(), barcodes)/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${DIR}-cs/${VERSION}/lib/python/cellranger/molecule_counter.py
		fi
		@@ -888,7 +890,8 @@ if [[ $setup == "true" ]]; then
		#if cellranger version is 3 or greater, restore assert functions
		if [[ `printf '%s\n' '$VERSION 3.0.0' \| sort -V \| head -n 1` != $VERSION ]]; then
		#disable functions if 10x technology run previously
		if [[ $lastcall != "10x" ]]; then
		if [[ $lastcall == "10x" ]]; then
		sed -i "s/if gem_group == prev_gem_group/#if gem_group == prev_gem_group/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/assert barcode_idx >= prev_barcode_idx/#assert barcode_idx >= prev_barcode_idx/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/assert np.array_equal(in_mc.get_barcodes(), barcodes)/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${DIR}-cs/${VERSION}/lib/python/cellranger/molecule_counter.py
		fi

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