Commit da4c646c authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

create separate test jobs for local and remote testing (disk space limit on GH Actions)

parent 0a90e1c9

test/run_tests_10x_gh_actions.sh

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#!/bin/bash



# run tests in universc directory (parent of test directory)

cd $(dirname ${BASH_SOURCE[0]})/..

pwd



# used to export to PATH for testing on SGE server

export PATH=${HOME}/local/bin/cellranger-2.1.0:$PATH



cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`



# set up cellranger reference

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi



# used to export to PATH for testing on SGE server

export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH



cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`



# set up cellranger reference

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi



# reset barcodes for test

bash launch_universc.sh -t "10x" --setup



## test 10x data

# unzip input data

ls ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt*

if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then

    gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

if [[ -d tiny-test ]]; then

    rm -rf tiny-test

fi

# test cellranger call

if [[ $cellrangerversion == "3.0.2" ]]; then

    cellranger testrun --id="tiny-test"

fi

# unzip input data

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz ]]; then

    gunzip -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz

fi

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq ]]; then

    rm -rf test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz

fi

# test cellranger call

if [[ -d tiny-count-v3 ]]; then

    rm -rf tiny-count-v3

fi

if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then

    gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt ]]; then

    rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

cellranger count --id="tiny-count-v3" \

 --fastqs="test/shared/cellranger-tiny-fastq/3.0.0/" --sample="tinygex" \

 --transcriptome="test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --jobmode "local" --localcores 1 

if [[ -d tiny-count-v2 ]]; then

    rm -rf tiny-count-v2

fi 

if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then

    gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt ]]; then

    rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

cellranger count --id="tiny-count-v2" \

 --fastqs="test/shared/cellranger-tiny-fastq/1.2.0/" --sample="" --chemistry="threeprime" \

 --transcriptome="test/cellranger_reference/cellranger-tiny-ref/1.2.0" \

 --jobmode "local" --localcores 1 



# call convert on 10x with multiple lanes

if [[ -d test-10x-v3 ]]; then

    rm -rf test-10x-v3

fi

if [[ -d input4cellranger_test-10x-v3 ]]; then

    rm -rf input4cellranger_test-10x-v3

fi

# unzip input data

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001/*fastq.gz ]]; then

    unpigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001/*fastq.gz

fi

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002/*fastq.gz ]]; then

    unpigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002/*fastq.gz

fi

bash launch_universc.sh --id "test-10x-v3" --technology "10x" \

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

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

 "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002" \

  --jobmode "local" --localcores 1 



# compress all input files

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq ]]; then

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

fi

test/run_tests_10x_local.sh

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#!/bin/bash



# run tests in universc directory (parent of test directory)

cd $(dirname ${BASH_SOURCE[0]})/..

pwd



# used to export to PATH for testing on SGE server

export PATH=${HOME}/local/bin/cellranger-2.1.0:$PATH



cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`



# set up cellranger reference

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi



# used to export to PATH for testing on SGE server

export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH



cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`



# set up cellranger reference

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi



# reset barcodes for test

bash launch_universc.sh -t "10x" --setup



## test 10x data

# unzip input data

ls ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt*

if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then

    gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

if [[ -d tiny-test ]]; then

    rm -rf tiny-test

fi

# test cellranger call

if [[ $cellrangerversion == "3.0.2" ]]; then

    cellranger testrun --id="tiny-test"

fi

# unzip input data

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz ]]; then

    gunzip -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz

fi

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq ]]; then

    rm -rf test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz

fi

# test cellranger call

if [[ -d tiny-count-v3 ]]; then

    rm -rf tiny-count-v3

fi

if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then

    gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt ]]; then

    rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

cellranger count --id="tiny-count-v3" \

 --fastqs="test/shared/cellranger-tiny-fastq/3.0.0/" --sample="tinygex" \

 --transcriptome="test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --jobmode "local" --localcores 1 

if [[ -d tiny-count-v2 ]]; then

    rm -rf tiny-count-v2

fi 

if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then

    gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt ]]; then

    rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

cellranger count --id="tiny-count-v2" \

 --fastqs="test/shared/cellranger-tiny-fastq/1.2.0/" --sample="" --chemistry="threeprime" \

 --transcriptome="test/cellranger_reference/cellranger-tiny-ref/1.2.0" \

 --jobmode "local" --localcores 1 



# call convert on 10x with multiple lanes

if [[ -d test-10x-v3 ]]; then

    rm -rf test-10x-v3

fi

if [[ -d input4cellranger_test-10x-v3 ]]; then

    rm -rf input4cellranger_test-10x-v3

fi

# unzip input data

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001/*fastq.gz ]]; then

    unpigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001/*fastq.gz

fi

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002/*fastq.gz ]]; then

    unpigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002/*fastq.gz

fi

bash launch_universc.sh --id "test-10x-v3" --technology "10x" \

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

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

 "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002" \

  --jobmode "local" --localcores 1 



# compress all input files

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq ]]; then

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

fi

test/run_tests_dropseq_gh_actions.sh

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#!/bin/bash



# run tests in universc directory (parent of test directory)

cd $(dirname ${BASH_SOURCE[0]})/..

pwd



# used to export to PATH for testing on SGE server

export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH



cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`



# set up cellranger reference

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi



## test drop-seq data

# unzip input data

if [[ -f test/shared/dropseq-test/*fastq.gz ]]; then

    unpigz -f test/shared/dropseq-test/*fastq.gz

fi

# test manual setup

bash launch_universc.sh -t "nadia" --setup



# remove processed files

if [[ -f SRR1873277_S1_L001_R[12]_001.fastq ]]; then

    rm SRR1873277_S1_L001_R[12]_001.fastq

fi

if [[ -d input4cellranger_test-dropseq ]]; then

    rm -rf input4cellranger_test-dropseq

fi

if [[ -d test-dropseq ]]; then

    rm -rf test-dropseq

fi



# call on dropseq with files

bash launch_universc.sh --id "test-dropseq" --technology "nadia" \

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

 --read1 "test/shared/dropseq-test/SRR1873277_Sample1_R1" \

 --read2 "test/shared/dropseq-test/SRR1873277_Sample1_R2" \

 --jobmode "local" --localcores 1 



# reset test data (compress)

 if [[ -f test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R1_001.fastq ]]; then

   gzip -f test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R1_001.fastq

fi

if [[ -f test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R2_001.fastq ]]; then

    gzip -f test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R2_001.fastq

fi

# reset test data (files names)

if [[ ! -f test/shared/dropseq-test/SRR1873277_Sample1_R1.fastq.gz ]]; then

    mv test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R1_001.fastq.gz test/shared/dropseq-test/SRR1873277_Sample1_R1.fastq.gz

else

    rm test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R1_001.fastq.gz

fi

if [[ ! -f test/shared/dropseq-test/SRR1873277_Sample1_R2.fastq.gz ]]; then

    mv test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R2_001.fastq.gz test/shared/dropseq-test/SRR1873277_Sample1_R2.fastq.gz

else

    rm test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R2_001.fastq.gz

fi



# compress all input files

if [[ -f test/shared/dropseq-test/*fastq ]]; then

    gzip test/shared/dropseq-test/*fastq

fi

test/run_tests_dropseq_local.sh

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#!/bin/bash



# run tests in universc directory (parent of test directory)

cd $(dirname ${BASH_SOURCE[0]})/..

pwd



# used to export to PATH for testing on SGE server

export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH



cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`



# set up cellranger reference

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi



## test drop-seq data

# unzip input data

if [[ -f test/shared/dropseq-test/*fastq.gz ]]; then

    unpigz -f test/shared/dropseq-test/*fastq.gz

fi

# test manual setup

bash launch_universc.sh -t "nadia" --setup



# remove processed files

if [[ -f SRR1873277_S1_L001_R[12]_001.fastq ]]; then

    rm SRR1873277_S1_L001_R[12]_001.fastq

fi

if [[ -d input4cellranger_test-dropseq ]]; then

    rm -rf input4cellranger_test-dropseq

fi

if [[ -d test-dropseq ]]; then

    rm -rf test-dropseq

fi



# call on dropseq with files

bash launch_universc.sh --id "test-dropseq" --technology "nadia" \

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

 --read1 "test/shared/dropseq-test/SRR1873277_Sample1_R1" \

 --read2 "test/shared/dropseq-test/SRR1873277_Sample1_R2" \

 --jobmode "local" --localcores 1 



# reset test data (compress)

 if [[ -f test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R1_001.fastq ]]; then

   gzip -f test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R1_001.fastq

fi

if [[ -f test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R2_001.fastq ]]; then

    gzip -f test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R2_001.fastq

fi

# reset test data (files names)

if [[ ! -f test/shared/dropseq-test/SRR1873277_Sample1_R1.fastq.gz ]]; then

    mv test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R1_001.fastq.gz test/shared/dropseq-test/SRR1873277_Sample1_R1.fastq.gz

else

    rm test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R1_001.fastq.gz

fi

if [[ ! -f test/shared/dropseq-test/SRR1873277_Sample1_R2.fastq.gz ]]; then

    mv test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R2_001.fastq.gz test/shared/dropseq-test/SRR1873277_Sample1_R2.fastq.gz

else

    rm test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R2_001.fastq.gz

fi



# compress all input files

if [[ -f test/shared/dropseq-test/*fastq ]]; then

    gzip test/shared/dropseq-test/*fastq

fi

test/run_tests_icell8_gh_actions.sh

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#!/bin/bash



# run tests in universc directory (parent of test directory)

cd $(dirname ${BASH_SOURCE[0]})/..

pwd



# used to export to PATH for testing on SGE server

export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH



cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`



# set up cellranger reference

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi



unpigz -k test/shared/icell8-test/72618_KU812*fastq.gz



if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq*

fi

if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq*

fi

if [ -f test/shared/icell8-test/72618_KU812_S2_L002_R1_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_KU812_S2_L002_R1_001.fastq*

fi

if [ -f test/shared/icell8-test/72618_KU812_S2_L002_R2_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_KU812_S2_L002_R2_001.fastq*

fi

if [ -d test-icell8-72618-KU812-2-lanes ];then

    rm -rf test-icell8-72618_KU812-2-lanes

fi

bash launch_universc.sh --id "test-icell8-72618_KU812-2-lanes" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R2_001.fastq" \

 --barcodefile "test/shared/icell8-test/WellList.txt" \

 --jobmode "local" --localcores 1 

if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq*

fi

if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R2_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R2_001.fastq*

fi

if [ -f test/shared/icell8-test/72618_KU812_S1_L002_R1_001.fastq ]; then

    rename "s/_S2_L002/_L002/" test/shared/icell8-test/72618_KU812_S2_L002_R1_001.fastq*

fi

if [ -f test/shared/icell8-test/72618_KU812_S1_L002_R2_001.fastq ]; then

    rename "s/_S2_L002/_L002/" test/shared/icell8-test/72618_KU812_S2_L002_R2_001.fastq*

fi

if [ -d test-icell8-72618_KU812-1-lane ]; then

    rm -rf test-icell8-72618_KU812-1-lane

fi

bash launch_universc.sh --id "test-icell8-72618_KU812-1-lane" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" \

 --barcodefile "test/shared/icell8-test/WellList.txt" \

 --jobmode "local" --localcores 1 

if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq*

fi

if [ -f test/shared/icell8-test/KU812_S1_L001_R2_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R2_001.fastq*

fi

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