Loading CHANGELOG +10 −0 Original line number Diff line number Diff line ### 1.2.4 - enables unit testing via nextflow for nf-core module - removes forced "auto" chemistry for 10x technology (allows setting for test fies too small for automated detection) - sets default values for last call parameters to 10x technology if not found (allows runs without errors on 1st call) - enables computing RNA offset parameters without warning messages (supports containerised workflows) ### 1.2.3 - enables GitHub citation widget Loading launch_universc.sh +30 −5 Original line number Diff line number Diff line Loading @@ -84,6 +84,16 @@ PERCELLSTATS=${TOOLS}/ExtractBasicStats.pl #####define set options##### # set defaults to 10x if missing (enables unit testing without warnings) if [[ -z ${lastcall_b} ]]; then lastcall_b=16 fi if [[ -z ${lastcall_u} ]]; then lastcall_u=10 fi if [[ -z ${lastcall_p} ]]; then lastcall_p="default:10x" fi lockfile=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.lock #path for .lock file lastcallfile=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.last_called #path for .last_called lastcall=`[[ -e $lastcallfile ]] && cat $lastcallfile || echo ""` Loading Loading @@ -2159,16 +2169,27 @@ if [[ "$technology" == "10x" ]]; then echo "Accepted chemistry: $chemistry" barcode_default=14 umi_default=10 elif [[ "$chemistry" == "SC3Pv2" ]]; then echo "Accepted chemistry: $chemistry" barcode_default=16 umi_default=10 elif [[ "$chemistry" == "SC3Pv3" ]]; then echo "Accepted chemistry: $chemistry" barcode_default=16 umi_default=12 elif [[ "$chemistry" != "auto" ]]; then #use automatic chemistry detection echo "Detecting 10x chemistry automatically" chemistry="auto" #do not convert UMI umi_default=12 fi # disable conversion for 10x barcodelength=${barcode_default} barrcodeadjust=0 umilength=${umi_default} umiadjust=0 fi fi if [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "icell8-5-prime" ]]; then if [[ $verbose ]]; then echo " Using $chemistry for $technology" Loading Loading @@ -2520,7 +2541,11 @@ if [[ $lock -eq 0 ]]; then echo "lastcall: b ${lastcall_b} u ${lastcall_u}; current: b ${barcodelength} u ${umilength}" echo "${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py" fi old_rna_offset=`echo $((${lastcall_b} + ${lastcall_u})) || 26` if [[ -z ${lastcall_b} ]] || [[ -z ${lastcall_u} ]]; then old_rna_offset=26 else old_rna_offset=`echo $((${lastcall_b} + ${lastcall_u}))` 2>%1 1> /dev/null fi new_rna_offset=`echo $((${barcodelength} + ${umilength}))` #convert barcodes back if last technology barcode greater than 16 bp Loading Loading
CHANGELOG +10 −0 Original line number Diff line number Diff line ### 1.2.4 - enables unit testing via nextflow for nf-core module - removes forced "auto" chemistry for 10x technology (allows setting for test fies too small for automated detection) - sets default values for last call parameters to 10x technology if not found (allows runs without errors on 1st call) - enables computing RNA offset parameters without warning messages (supports containerised workflows) ### 1.2.3 - enables GitHub citation widget Loading
launch_universc.sh +30 −5 Original line number Diff line number Diff line Loading @@ -84,6 +84,16 @@ PERCELLSTATS=${TOOLS}/ExtractBasicStats.pl #####define set options##### # set defaults to 10x if missing (enables unit testing without warnings) if [[ -z ${lastcall_b} ]]; then lastcall_b=16 fi if [[ -z ${lastcall_u} ]]; then lastcall_u=10 fi if [[ -z ${lastcall_p} ]]; then lastcall_p="default:10x" fi lockfile=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.lock #path for .lock file lastcallfile=${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/.last_called #path for .last_called lastcall=`[[ -e $lastcallfile ]] && cat $lastcallfile || echo ""` Loading Loading @@ -2159,16 +2169,27 @@ if [[ "$technology" == "10x" ]]; then echo "Accepted chemistry: $chemistry" barcode_default=14 umi_default=10 elif [[ "$chemistry" == "SC3Pv2" ]]; then echo "Accepted chemistry: $chemistry" barcode_default=16 umi_default=10 elif [[ "$chemistry" == "SC3Pv3" ]]; then echo "Accepted chemistry: $chemistry" barcode_default=16 umi_default=12 elif [[ "$chemistry" != "auto" ]]; then #use automatic chemistry detection echo "Detecting 10x chemistry automatically" chemistry="auto" #do not convert UMI umi_default=12 fi # disable conversion for 10x barcodelength=${barcode_default} barrcodeadjust=0 umilength=${umi_default} umiadjust=0 fi fi if [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "icell8-5-prime" ]]; then if [[ $verbose ]]; then echo " Using $chemistry for $technology" Loading Loading @@ -2520,7 +2541,11 @@ if [[ $lock -eq 0 ]]; then echo "lastcall: b ${lastcall_b} u ${lastcall_u}; current: b ${barcodelength} u ${umilength}" echo "${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py" fi old_rna_offset=`echo $((${lastcall_b} + ${lastcall_u})) || 26` if [[ -z ${lastcall_b} ]] || [[ -z ${lastcall_u} ]]; then old_rna_offset=26 else old_rna_offset=`echo $((${lastcall_b} + ${lastcall_u}))` 2>%1 1> /dev/null fi new_rna_offset=`echo $((${barcodelength} + ${umilength}))` #convert barcodes back if last technology barcode greater than 16 bp Loading
