Loading launch_universc.sh +11 −2 Original line number Diff line number Diff line Loading @@ -82,8 +82,9 @@ Mandatory arguments to long options are mandatory for short options too. Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 Sci-Seq (8bp UMI, 10bp barcode): sciseq Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq SeqWell (12bp barcode, 8bp UMI): seqwell Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_" e.g. Custom (16bp barcode, 10bp UMI): custom_16_10 Loading Loading @@ -500,6 +501,10 @@ if [[ "$technology" == "scrbseq" ]] || [[ "$technology" == "scrb-seq" ]] || [[ " echo "Running with SCRB-Seq / mcSCRB-seq parameters" technology="scrbseq" fi if [[ "$technology" == "seqwell" ]] || [[ "$technology" == "seq-well" ]]; then echo "Running with Sci-Seq-Well parameters" technology="seqwell" fi if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smart-seq" ]] || [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smart-seq2" ]] || [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smart-seq2-umi" ]] || [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "smart-seq3" ]]; then echo "Running with Smart-Seq3 parameters (version 3 with UMIs)" echo "***WARNING: Smart-Seq settings should only be used for kits that have UMIs***" Loading Loading @@ -532,6 +537,7 @@ if [[ "$technology" != "10x" ]] \ && [[ "$technology" != "quartz-seq2"* ]] \ && [[ "$technology" != "sciseq" ]] \ && [[ "$technology" != "scrbseq" ]] \ && [[ "$technology" != "seqwell" ]] \ && [[ "$technology" != "smart-seq"* ]]\ && [[ "$technology" != "surecell" ]]; then if [[ "$technology" != "custom"* ]]; then Loading Loading @@ -793,7 +799,7 @@ else echo "***WARNING: barcodes not available for Smart-Seq 2 or 3, using iCELL8 whitelist (version 3)***" echo "...valid barcodes may be an overestimate" barcodefile=${SDIR}/iCell8_barcode.txt elif [[ "$technology" == "custom"* ]] || [[ "$technology" == "celseq"* ]] || [[ "$technology" == "scrbseq" ]] || [[ "$technology" == "sciseq" ]] || [[ "$technology" == "surecell" ]]; then elif [[ "$technology" == "custom"* ]] || [[ "$technology" == "celseq"* ]] || [[ "$technology" == "sciseq" ]] || [[ "$technology" == "scrbseq" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "surecell" ]]; then if [[ "$technology" == "celseq" ]]; then customname="celseq" minlength=8 Loading @@ -806,6 +812,9 @@ else elif [[ "$technology" == "scrbseq" ]]; then customname="scrbseq" minlength=6 elif [[ "$technology" == "seqwell" ]]; then customname="seqwell" minlength=12 elif [[ "$technology" == "surecell" ]]; then customname="surecell" barcodelength=18 Loading Loading
launch_universc.sh +11 −2 Original line number Diff line number Diff line Loading @@ -82,8 +82,9 @@ Mandatory arguments to long options are mandatory for short options too. Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 Sci-Seq (8bp UMI, 10bp barcode): sciseq Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq SeqWell (12bp barcode, 8bp UMI): seqwell Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_" e.g. Custom (16bp barcode, 10bp UMI): custom_16_10 Loading Loading @@ -500,6 +501,10 @@ if [[ "$technology" == "scrbseq" ]] || [[ "$technology" == "scrb-seq" ]] || [[ " echo "Running with SCRB-Seq / mcSCRB-seq parameters" technology="scrbseq" fi if [[ "$technology" == "seqwell" ]] || [[ "$technology" == "seq-well" ]]; then echo "Running with Sci-Seq-Well parameters" technology="seqwell" fi if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smart-seq" ]] || [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smart-seq2" ]] || [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smart-seq2-umi" ]] || [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "smart-seq3" ]]; then echo "Running with Smart-Seq3 parameters (version 3 with UMIs)" echo "***WARNING: Smart-Seq settings should only be used for kits that have UMIs***" Loading Loading @@ -532,6 +537,7 @@ if [[ "$technology" != "10x" ]] \ && [[ "$technology" != "quartz-seq2"* ]] \ && [[ "$technology" != "sciseq" ]] \ && [[ "$technology" != "scrbseq" ]] \ && [[ "$technology" != "seqwell" ]] \ && [[ "$technology" != "smart-seq"* ]]\ && [[ "$technology" != "surecell" ]]; then if [[ "$technology" != "custom"* ]]; then Loading Loading @@ -793,7 +799,7 @@ else echo "***WARNING: barcodes not available for Smart-Seq 2 or 3, using iCELL8 whitelist (version 3)***" echo "...valid barcodes may be an overestimate" barcodefile=${SDIR}/iCell8_barcode.txt elif [[ "$technology" == "custom"* ]] || [[ "$technology" == "celseq"* ]] || [[ "$technology" == "scrbseq" ]] || [[ "$technology" == "sciseq" ]] || [[ "$technology" == "surecell" ]]; then elif [[ "$technology" == "custom"* ]] || [[ "$technology" == "celseq"* ]] || [[ "$technology" == "sciseq" ]] || [[ "$technology" == "scrbseq" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "surecell" ]]; then if [[ "$technology" == "celseq" ]]; then customname="celseq" minlength=8 Loading @@ -806,6 +812,9 @@ else elif [[ "$technology" == "scrbseq" ]]; then customname="scrbseq" minlength=6 elif [[ "$technology" == "seqwell" ]]; then customname="seqwell" minlength=12 elif [[ "$technology" == "surecell" ]]; then customname="surecell" barcodelength=18 Loading
