Commit 2d05ad23 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

enable version 3 chemistry for 10x

parent e5527c13

launch_universc.sh

+2 −2
Original line number Diff line number Diff line
@@ -707,8 +707,8 @@ elif ! [[ $mem =~ $int ]] && [[ $setup == "false" ]]; then 
fi



#check if chemistry matches expected input

if [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then

    echo "Error: option --chemistry must be SC3Pv2, SC5P-PE , or SC5P-R2"

if [[ "$chemistry" != "SC3Pv3" ]] && [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then

    echo "Error: option --chemistry must be SC3Pv3, SC3Pv2, SC5P-PE , or SC5P-R2"

    exit 1

fi

run_tests.sh

+3 −1
Original line number Diff line number Diff line
@@ -32,6 +32,7 @@ cellranger count --id="tiny-count-v2" \ 
# call convert on 10x with multiple lanes

bash /universc/launch_universc.sh --id "test-10x" --technology "10x" \

 --reference "/universc/test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --chemistry "SC3Pv3" \

 --file "/universc/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001" \

 "/universc/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002"
@@ -44,7 +45,8 @@ bash /universc/launch_universc.sh -t "nadia" --setup 
bash /universc/launch_universc.sh --id "test-dropseq" --technology "nadia" \

 --reference "/universc/test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --read1 "/universc/test/shared/dropseq-test/SRR1873277_S1_L001_R1_001" \

 --read2 "/universc/test/shared/dropseq-test/SRR1873277_S1_L001_R2_001" 

 --read2 "/universc/test/shared/dropseq-test/SRR1873277_S1_L001_R2_001" \

 --chemistry "SCP-V3"



## test icell8 data

# unzip input data

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