Commit 6b4ef0bd authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

Merge branch 'master' of github.com:TomKellyGenetics/cellranger_convert

parents 64de1ebd b19a16f1

launch_universc.sh

+3 −3
Original line number Diff line number Diff line
@@ -389,15 +389,15 @@ if [[ $testrun == "true" ]]; then 
    description=${id}

    

    if [[ $technology == "10x" ]]; then

        gunzip -k ${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L00[12]_R[12]_001.fastq.gz

        gunzip -fk ${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L00[12]_R[12]_001.fastq.gz

        read1=("${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq" "${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq")

        read2=("${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_002.fastq" "${SDIR}/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq")

    elif [[ $technology == "nadia" ]]; then

        gunzip -k ${SDIR}/test/shared/dropseq-test/SRR1873277_S1_L001_R[12]_001.fastq

        gunzip -fk ${SDIR}/test/shared/dropseq-test/SRR1873277_S1_L001_R[12]_001.fastq.gz

        read1=("${SDIR}/test/shared/dropseq-test/SRR1873277_S1_L001_R1_001.fastq")

        read2=("${SDIR}/test/shared/dropseq-test/SRR1873277_S1_L001_R2_001.fastq")

    elif [[ $technology == "icell8" ]]; then

        gunzip -k ${SDIR}/test/shared/mappa-test/test_FL_R[12].fastq.gz

        gunzip -fk ${SDIR}/test/shared/mappa-test/test_FL_R[12].fastq.gz

        read1=("${SDIR}/test/shared/mappa-test/test_FL_R1.fastq")

        read2=("${SDIR}/test/shared/mappa-test/test_FL_R2.fastq")

    else

run_tests.sh

+23 −10
Original line number Diff line number Diff line
@@ -32,12 +32,16 @@ cellranger count --id="tiny-count-v2" \ 
 --transcriptome="/cellranger-3.0.2.9001/cellranger-tiny-ref/1.2.0"



# call convert on 10x with multiple lanes

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

bash /universc/launch_universc.sh --id "test-10x-v3" --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"



bash /universc/launch_universc.sh --id "test-10x-v2" --technology "10x" \

 --reference "/universc/test/cellranger_reference/cellranger-tiny-ref/1.2.0" \

 --file "/universc/test/shared/cellranger-tiny-fastq/1.2.0/tinygex_S1_L001" \

 "/universc/test/shared/cellranger-tiny-fastq/1.2.0/tinygex_S1_L002"



## test drop-seq data

# unzip input data

gunzip /universc/test/shared/dropseq-test/*fastq.gz
@@ -47,25 +51,34 @@ 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" \

 --chemistry "SCP-V3"

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



## test icell8 data

# unzip input data

gunzip /universc/test/shared/mappa-test/*fastq.gz

# call on icell8 files with custom whitelist and non-standard file names

gunzip -fk /universc/test/shared/mappa-test/*fastq.gz

# call on icell8 files with default whitelist

bash /universc/launch_universc.sh --id "test-icell8" --technology "iCell8" \

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

 --read1 "/universc/test/shared/mappa-test/test_FL_R1.fastq" \

 --read2 "/universc/test/shared/mappa-test/test_FL_R2.fastq" \

 --barcodefile "/universc/test/shared/mappa-test/99999_mappa_test_selected_WellList.TXT"

 --chemistry "SC3Pv2"

#restore file names for test job

mv /universc/test/shared/mappa-test/test_FL_S1_L001_R1_001.fastq /universc/test/shared/mappa-test/test_FL_R1.fastq

mv /universc/test/shared/mappa-test/test_FL_S1_L001_R2_001.fastq /universc/test/shared/mappa-test/test_FL_R2.fastq



# call on icell8 files with custom whitelist and non-standard file names

bash /universc/launch_universc.sh --id "test-icell8-custom" --technology "iCell8" \

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

 --read1 "/universc/test/shared/mappa-test/test_FL_R1.fastq" \

 --read2 "/universc/test/shared/mappa-test/test_FL_R2.fastq" \

 --barcodefile "/universc/test/shared/mappa-test/mappa_barcodes.txt"  \

 --chemistry "SC3Pv2"

#restore file names for test job

mv /universc/test/shared/mappa-test/test_FL_S1_L001_R1_001.fastq /universc/test/shared/mappa-test/test_FL_R1.fastq

mv /universc/test/shared/mappa-test/test_FL_S1_L001_R2_001.fastq /universc/test/shared/mappa-test/test_FL_R2.fastq



# compress all input files

gzip /universc/test/shared/cellranger-tiny-fastq/3.0.0/*fastq

gzip /universc/test/shared/dropseq-test/*fastq

gzip /universc/test/shared/mappa-test/*fastq

gzip -f /universc/test/shared/cellranger-tiny-fastq/3.0.0/*fastq

gzip -f /universc/test/shared/dropseq-test/*fastq

gzip -f /universc/test/shared/mappa-test/*fastq

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