Loading launch_universc.sh +5 −5 Original line number Diff line number Diff line Loading @@ -670,11 +670,11 @@ elif [[ "$technology" == "icell8-full" ]] || [[ "$technology" == "icell8-fl" ]] fi chemistry="SC5P-PE" fi elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrops-v1" ]] || [[ "$technology" == "indropv1" ]] || [[ "$technology" == "indropsv1" ]] || [[ "$technology" == "1cellbio-v1" ]] || [[ "$technology" == "1cellbiov1" ]]; then elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrops-v1" ]] || [[ "$technology" == "indropv1" ]] || [[ "$technology" == "indropsv1" ]] || [[ "$technology" == "indrop1" ]] || [[ "$technology" == "indrops1" ]] || [[ "$technology" == "1cellbio-v1" ]] || [[ "$technology" == "1cellbiov1" ]]; then technology="indrop-v1" elif [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrops-v2" ]] || [[ "$technology" == "indropv2" ]] || [[ "$technology" == "indropsv2" ]] || [[ "$technology" == "1cellbio-v2" ]] || [[ "$technology" == "1cellbiov2" ]]; then elif [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrops-v2" ]] || [[ "$technology" == "indropv2" ]] || [[ "$technology" == "indropsv2" ]] || [[ "$technology" == "indrop2" ]] || [[ "$technology" == "indrops2" ]] ||[[ "$technology" == "1cellbio-v2" ]] || [[ "$technology" == "1cellbiov2" ]]; then technology="indrop-v2" elif [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "indrops-v3" ]] || [[ "$technology" == "indropv3" ]] || [[ "$technology" == "indropsv3" ]] || [[ "$technology" == "1cellbio-v3" ]] || [[ "$technology" == "1cellbiov3" ]]; then elif [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "indrops-v3" ]] || [[ "$technology" == "indropv3" ]] || [[ "$technology" == "indropsv3" ]] || [[ "$technology" == "indrop3" ]] || [[ "$technology" == "indrops3" ]] || [[ "$technology" == "1cellbio-v3" ]] || [[ "$technology" == "1cellbiov3" ]]; then technology="indrop-v3" elif [[ "$technology" == "marsseq" ]] || [[ "$technology" == "mars-seq" ]] || [[ "$technology" == "marsseq-v1" ]] || [[ "$technology" == "mars-seq-v1" ]] || [[ "$technology" == "marsseqv1" ]] || [[ "$technology" == "mars-seqv1" ]]; then technology="marsseq-v1" Loading Loading @@ -2916,8 +2916,8 @@ else for convFile in "${convFiles[@]}"; do #remove adapter if present sed -E ' /(.{8,8}?).{22}(.{8})(.{6})T{1,}$/ { s/.*?(.{8,8}?).{22}(.{8})(.{6})T{1,}$/\1\2\3/g /^.*(.{8})GA.................CTT(.{8})(.{6}).*$/ { s/^.*(.{8})GA.................CTT(.{8})(.{6}).*$/\1\2\3/g n n s/^(.{8}).{22}(.{8})(.{6}).*/\1\2\3/g Loading sub/MakeIndropBarcodes.pl +12 −8 Original line number Diff line number Diff line Loading @@ -34,19 +34,23 @@ my $length = scalar (@list1); my @list12; if ($version =~ m/v1/) { for (my $i = 0; $i < $length; $i++) { my $element1 = substr ($list1[$i], 0, 8); my $element12 = $element1.$list2[$i]; foreach my $element1 (@list1) { $element1 = substr ($element1, 0, 8); foreach my $element2 (@list2) { my $element12 = $element1.$element2; push (@list12, $element12); } } } elsif ($version =~ m/v2/) { for (my $i = 0; $i < $length; $i++) { my $element1 = substr ($list1[$i], 0, 8); my $element12 = $element1.$list2[$i]; foreach my $element1 (@list1) { $element1 = substr ($element1, 0, 8); foreach my $element2 (@list2) { my $element12 = $element1.$element2; push (@list12, $element12); } } } elsif ($version =~ m/v3/) { foreach my $element1 (@list1) { $element1 = substr ($element1, 0, 8); Loading test/run_tests_indropsv1v2_local.sh 0 → 100644 +17 −0 Original line number Diff line number Diff line #! /bin/bash bash launch_universc.sh --id "test-in-v2" --technology "indrop2" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --file "/home/tom/datasets/indropsv2_public_data/lib1_L001" \ "/home/tom/datasets/indropsv2_public_data/lib1_L002" "/home/tom/datasets/indropsv2_public_data/lib1_L003" "/home/tom/datasets/indropsv2_public_data/lib1_L004" \ --per-cell-data --jobmode "local" --localcores 8 bash launch_universc.sh --id "test-in-v1" --technology "indrop1" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --file "/home/tom/datasets/indropsv1_public_data/sample_S1_L001" \ --per-cell-data --jobmode "local" --localcores 8 rename "s/S1_L001/L001/" /home/tom/datasets/indropsv2_public_data/sample*fastq rename "s/S2_L002/L002/" /home/tom/datasets/indropsv2_public_data/sample*fastq rename "s/S3_L003/L003/" /home/tom/datasets/indropsv2_public_data/sample*fastq rename "s/S4_L004/L004/" /home/tom/datasets/indropsv2_public_data/sample*fastq Loading
launch_universc.sh +5 −5 Original line number Diff line number Diff line Loading @@ -670,11 +670,11 @@ elif [[ "$technology" == "icell8-full" ]] || [[ "$technology" == "icell8-fl" ]] fi chemistry="SC5P-PE" fi elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrops-v1" ]] || [[ "$technology" == "indropv1" ]] || [[ "$technology" == "indropsv1" ]] || [[ "$technology" == "1cellbio-v1" ]] || [[ "$technology" == "1cellbiov1" ]]; then elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrops-v1" ]] || [[ "$technology" == "indropv1" ]] || [[ "$technology" == "indropsv1" ]] || [[ "$technology" == "indrop1" ]] || [[ "$technology" == "indrops1" ]] || [[ "$technology" == "1cellbio-v1" ]] || [[ "$technology" == "1cellbiov1" ]]; then technology="indrop-v1" elif [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrops-v2" ]] || [[ "$technology" == "indropv2" ]] || [[ "$technology" == "indropsv2" ]] || [[ "$technology" == "1cellbio-v2" ]] || [[ "$technology" == "1cellbiov2" ]]; then elif [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrops-v2" ]] || [[ "$technology" == "indropv2" ]] || [[ "$technology" == "indropsv2" ]] || [[ "$technology" == "indrop2" ]] || [[ "$technology" == "indrops2" ]] ||[[ "$technology" == "1cellbio-v2" ]] || [[ "$technology" == "1cellbiov2" ]]; then technology="indrop-v2" elif [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "indrops-v3" ]] || [[ "$technology" == "indropv3" ]] || [[ "$technology" == "indropsv3" ]] || [[ "$technology" == "1cellbio-v3" ]] || [[ "$technology" == "1cellbiov3" ]]; then elif [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "indrops-v3" ]] || [[ "$technology" == "indropv3" ]] || [[ "$technology" == "indropsv3" ]] || [[ "$technology" == "indrop3" ]] || [[ "$technology" == "indrops3" ]] || [[ "$technology" == "1cellbio-v3" ]] || [[ "$technology" == "1cellbiov3" ]]; then technology="indrop-v3" elif [[ "$technology" == "marsseq" ]] || [[ "$technology" == "mars-seq" ]] || [[ "$technology" == "marsseq-v1" ]] || [[ "$technology" == "mars-seq-v1" ]] || [[ "$technology" == "marsseqv1" ]] || [[ "$technology" == "mars-seqv1" ]]; then technology="marsseq-v1" Loading Loading @@ -2916,8 +2916,8 @@ else for convFile in "${convFiles[@]}"; do #remove adapter if present sed -E ' /(.{8,8}?).{22}(.{8})(.{6})T{1,}$/ { s/.*?(.{8,8}?).{22}(.{8})(.{6})T{1,}$/\1\2\3/g /^.*(.{8})GA.................CTT(.{8})(.{6}).*$/ { s/^.*(.{8})GA.................CTT(.{8})(.{6}).*$/\1\2\3/g n n s/^(.{8}).{22}(.{8})(.{6}).*/\1\2\3/g Loading
sub/MakeIndropBarcodes.pl +12 −8 Original line number Diff line number Diff line Loading @@ -34,19 +34,23 @@ my $length = scalar (@list1); my @list12; if ($version =~ m/v1/) { for (my $i = 0; $i < $length; $i++) { my $element1 = substr ($list1[$i], 0, 8); my $element12 = $element1.$list2[$i]; foreach my $element1 (@list1) { $element1 = substr ($element1, 0, 8); foreach my $element2 (@list2) { my $element12 = $element1.$element2; push (@list12, $element12); } } } elsif ($version =~ m/v2/) { for (my $i = 0; $i < $length; $i++) { my $element1 = substr ($list1[$i], 0, 8); my $element12 = $element1.$list2[$i]; foreach my $element1 (@list1) { $element1 = substr ($element1, 0, 8); foreach my $element2 (@list2) { my $element12 = $element1.$element2; push (@list12, $element12); } } } elsif ($version =~ m/v3/) { foreach my $element1 (@list1) { $element1 = substr ($element1, 0, 8); Loading
test/run_tests_indropsv1v2_local.sh 0 → 100644 +17 −0 Original line number Diff line number Diff line #! /bin/bash bash launch_universc.sh --id "test-in-v2" --technology "indrop2" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --file "/home/tom/datasets/indropsv2_public_data/lib1_L001" \ "/home/tom/datasets/indropsv2_public_data/lib1_L002" "/home/tom/datasets/indropsv2_public_data/lib1_L003" "/home/tom/datasets/indropsv2_public_data/lib1_L004" \ --per-cell-data --jobmode "local" --localcores 8 bash launch_universc.sh --id "test-in-v1" --technology "indrop1" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --file "/home/tom/datasets/indropsv1_public_data/sample_S1_L001" \ --per-cell-data --jobmode "local" --localcores 8 rename "s/S1_L001/L001/" /home/tom/datasets/indropsv2_public_data/sample*fastq rename "s/S2_L002/L002/" /home/tom/datasets/indropsv2_public_data/sample*fastq rename "s/S3_L003/L003/" /home/tom/datasets/indropsv2_public_data/sample*fastq rename "s/S4_L004/L004/" /home/tom/datasets/indropsv2_public_data/sample*fastq
