Commit 0a533a2e authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update test scripts for icell8

parent ff301b09

test/run_tests_icell8.sh

+3 −183
Original line number Original line Diff line number Diff line 
#!/bin/bash

#!/bin/bash





# run tests in home directory (writeable)

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

#cd ~

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

# run tests in universc directory

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

pwd

pwd



# used to export to PATH for testing on SGE server

# used to export to PATH for testing on SGE server

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

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')'`

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

cellrangerpath=`which cellranger`

cellrangerpath=`which cellranger`





## test icell8 data

# unzip input data

#gzip -k test/shared/icell8-test/*fastq

#gzip -k test/shared/icell8-test/*/*/*fastq 

#gunzip -k test/shared/icell8-test/*fastq

#gunzip -k test/shared/icell8-test/*/*/*fastq 

#if [[ -f test/shared/icell8-test/*fastq.gz ]]; then

#    gunzip -fk test/shared/icell8-test/*fastq.gz

#fi

if [ -d test-icell8-default ];then

    rm -rf test-icell8-default

fi

# call on icell8 files with default whitelist

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

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

 --read1 "test/shared/icell8-test/iCELL8_01_S1_L001_R1_001.fastq" "test/shared/icell8-test/iCELL8_01_S1_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/iCELL8_01_S1_L001_R2_001.fastq" "test/shared/icell8-test/iCELL8_01_S1_L002_R2_001.fastq" \

 --jobmode "sge"



if [ -d test-icell8-custom ];then

    rm -rf test-icell8-custom

fi

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

bash launch_universc.sh --setup -t "icell8"  --barcodefile "test/shared/icell8-test/BarcodeList.txt"

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

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

 --read1 "test/shared/icell8-test/iCELL8_01_S1_L001_R1_001.fastq" "test/shared/icell8-test/iCELL8_01_S1_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/iCELL8_01_S1_L001_R2_001.fastq" "test/shared/icell8-test/iCELL8_01_S1_L002_R2_001.fastq" \

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

 --jobmode "sge"



if [ -f test/shared/icell8-test/72618_A375_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_A375_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_A375_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_A375_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_A375_S2_L002_R1_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_A375_S2_L002_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_A375_S2_L002_R2_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_A375_S2_L002_R2_001.fastq

fi

if [ -d test-icell8-72618-A375-2-lanes ];then

    rm -rf test-icell8-72618-A375-2-lanes

fi

bash launch_universc.sh --id "test-icell8-72618_A375-2-lanes" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_A375_L001_R1_001.fastq" "test/shared/icell8-test/72618_A375_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_A375_L001_R2_001.fastq" "test/shared/icell8-test/72618_A375_L002_R2_001.fastq" \

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

 --jobmode "sge"

if [ -f test/shared/icell8-test/72618_A375_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_A375_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/A375_S1_L001_R2_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_A375_S1_L001_R2_001.fastq

fi

if [ -d test-icell8-A375-1-lane ];then

    rm -rf test-icell8-A375-1-lane

fi

bash launch_universc.sh --id "test-icell8-72618_A375-1-lane" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_A375_L001_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_A375_L001_R2_001.fastq" \

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

 --jobmode "sge"



if [ -f test/shared/icell8-test/72618_HCT116_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_HCT116_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_HCT116_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_HCT116_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_HCT116_S2_L002_R1_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_HCT116_S2_L002_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_HCT116_S2_L002_R2_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_HCT116_S2_L002_R2_001.fastq

fi

if [ -d test-icell8-72618-HCT116-2-lanes ];then

    rm -rf test-icell8-72618-HCT116-2-lanes

fi

bash launch_universc.sh --id "test-icell8-72618_HCT116-2-lanes" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_HCT116_L001_R1_001.fastq" "test/shared/icell8-test/72618_HCT116_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_HCT116_L001_R2_001.fastq" "test/shared/icell8-test/72618_HCT116_L002_R2_001.fastq" \

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

 --jobmode "sge"

if [ -f test/shared/icell8-test/72618_HCT116_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_HCT116_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/HCT116_S1_L001_R2_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_HCT116_S1_L001_R2_001.fastq

fi

if [ -d test-icell8-HCT116-1-lane ];then

    rm -rf test-icell8-HCT116-1-lane

fi

bash launch_universc.sh --id "test-icell8-72618_HCT116-1-lane" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_HCT116_L001_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_HCT116_L001_R2_001.fastq" \

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

 --jobmode "sge"



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

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

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

fi

fi
@@ -152,77 +46,3 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-1-lane" --technology "iCel 
 --read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" \

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

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

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

 --jobmode "sge"
 
 --jobmode "sge"
 


if [ -f test/shared/icell8-test/72618_NCI-H2452_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_NCI-H2452_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_NCI-H2452_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_NCI-H2452_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_NCI-H2452_S2_L002_R1_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_NCI-H2452_S2_L002_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_NCI-H2452_S2_L002_R2_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_NCI-H2452_S2_L002_R2_001.fastq

fi

if [ -d test-icell8-72618-NCI-H2452-2-lanes ];then

    rm -rf test-icell8-72618-NCI-H2452-2-lanes

fi

bash launch_universc.sh --id "test-icell8-72618_NCI-H2452-2-lanes" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_NCI-H2452_L001_R1_001.fastq" "test/shared/icell8-test/72618_NCI-H2452_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_NCI-H2452_L001_R2_001.fastq" "test/shared/icell8-test/72618_NCI-H2452_L002_R2_001.fastq" \

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

 --jobmode "sge"

if [ -f test/shared/icell8-test/72618_NCI-H2452_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_NCI-H2452_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/NCI-H2452_S1_L001_R2_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_NCI-H2452_S1_L001_R2_001.fastq

fi

if [ -d test-icell8-NCI-H2452-1-lane ];then

    rm -rf test-icell8-NCI-H2452-1-lane

fi

bash launch_universc.sh --id "test-icell8-72618_NCI-H2452-1-lane" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_NCI-H2452_L001_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_NCI-H2452_L001_R2_001.fastq" \

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

 --jobmode "sge"



if [ -f test/shared/icell8-test/test_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/test_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/test_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/test_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/test_S2_L002_R1_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/test_S2_L002_R1_001.fastq

fi

if [ -f test/shared/icell8-test/test_S2_L002_R2_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/test_S2_L002_R2_001.fastq

fi

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

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

fi

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

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

 --read1 "test/shared/icell8-test/test_L001_R1_001.fastq" "test/shared/icell8-test/test_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/test_L001_R2_001.fastq" "test/shared/icell8-test/test_L002_R2_001.fastq" \

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

 --jobmode "sge"

if [ -f test/shared/icell8-test/test_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/test_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/$_S1_L001_R2_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/test_S1_L001_R2_001.fastq

fi

if [ -d test-icell8-$-1-lane ];then

    rm -rf test-icell8-$-1-lane

fi

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

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

 --read1 "test/shared/icell8-test/test_L001_R1_001.fastq" \

 --read2 "test/shared/icell8-test/test_L001_R2_001.fastq" \

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

 --jobmode "sge"

test/run_tests_icell8_internal.sh

0 → 100644
+59 −0
Original line number Original line Diff line number Diff line 
#!/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`



## test on internal icell8 data

if [ -d test-icell8-default ];then

    rm -rf test-icell8-default

fi

if [ -f test/internal/icell8-test/iCELL8_01_S1_L001_R1_001.fastq.gz ]; then

     gunzip -k test/internal/icell8-test/iCELL8_01_S1_L001_R1_001.fastq.gz

fi

if [ -f test/internal/icell8-test/iCELL8_01_S1_L001_R2_001.fastq.gz ]; then

     gunzip -k test/internal/icell8-test/iCELL8_01_S1_L001_R2_001.fastq.gz

fi

if [ -f test/internal/icell8-test/iCELL8_01_S1_L002_R1_001.fastq.gz ]; then

    gunzip -k test/internal/icell8-test/iCELL8_01_S1_L002_R1_001.fastq.gz

fi

if [ -f test/internal/icell8-test/iCELL8_01_S1_L002_R2_001.fastq.gz ]; then

    gunzip -k test/internal/icell8-test/iCELL8_01_S1_L002_R2_001.fastq.gz

fi

# call on icell8 files with default whitelist

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

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

 --read1 "test/internal/icell8-test/iCELL8_01_S1_L001_R1_001.fastq" "test/internal/icell8-test/iCELL8_01_S1_L002_R1_001.fastq" \

 --read2 "test/internal/icell8-test/iCELL8_01_S1_L001_R2_001.fastq" "test/internal/icell8-test/iCELL8_01_S1_L002_R2_001.fastq" \

 --jobmode "sge"



if [ -d test-icell8-custom ];then

    rm -rf test-icell8-custom

fi

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

bash launch_universc.sh --setup -t "icell8"  --barcodefile "test/internal/icell8-test/BarcodeList.txt"

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

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

 --read1 "test/internal/icell8-test/iCELL8_01_S1_L001_R1_001.fastq" "test/internal/icell8-test/iCELL8_01_S1_L002_R1_001.fastq" \

 --read2 "test/internal/icell8-test/iCELL8_01_S1_L001_R2_001.fastq" "test/internal/icell8-test/iCELL8_01_S1_L002_R2_001.fastq" \

 --barcodefile "test/internal/icell8-test/BarcodeList.txt" \

 --jobmode "sge"



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

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

 --read1 "test/internal/icell8-test/test_L001_R1_001.fastq" "test/internal/icell8-test/test_L002_R1_001.fastq" \

 --read2 "test/internal/icell8-test/test_L001_R2_001.fastq" "test/internal/icell8-test/test_L002_R2_001.fastq" \

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

 --jobmode "sge"

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

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

 --read1 "test/internal/icell8-test/test_S1_L001_R1_001.fastq" \

 --read2 "test/internal/icell8-test/test_S2_L001_R2_001.fastq" \

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

 --jobmode "sge"

test/run_tests_icell8_public.sh

0 → 100644
+159 −0
Original line number Original line Diff line number Diff line 
#!/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`



if [ -f test/shared/icell8-test/72618_A375_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_A375_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_A375_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_A375_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_A375_S2_L002_R1_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_A375_S2_L002_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_A375_S2_L002_R2_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_A375_S2_L002_R2_001.fastq

fi

if [ -d test-icell8-72618-A375-2-lanes ];then

    rm -rf test-icell8-72618-A375-2-lanes

fi

bash launch_universc.sh --id "test-icell8-72618_A375-2-lanes" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_A375_L001_R1_001.fastq" "test/shared/icell8-test/72618_A375_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_A375_L001_R2_001.fastq" "test/shared/icell8-test/72618_A375_L002_R2_001.fastq" \

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

 --jobmode "sge"

if [ -f test/shared/icell8-test/72618_A375_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_A375_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/A375_S1_L001_R2_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_A375_S1_L001_R2_001.fastq

fi

if [ -d test-icell8-A375-1-lane ];then

    rm -rf test-icell8-A375-1-lane

fi

bash launch_universc.sh --id "test-icell8-72618_A375-1-lane" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_A375_L001_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_A375_L001_R2_001.fastq" \

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

 --jobmode "sge"



if [ -f test/shared/icell8-test/72618_HCT116_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_HCT116_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_HCT116_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_HCT116_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_HCT116_S2_L002_R1_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_HCT116_S2_L002_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_HCT116_S2_L002_R2_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_HCT116_S2_L002_R2_001.fastq

fi

if [ -d test-icell8-72618-HCT116-2-lanes ];then

    rm -rf test-icell8-72618-HCT116-2-lanes

fi

bash launch_universc.sh --id "test-icell8-72618_HCT116-2-lanes" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_HCT116_L001_R1_001.fastq" "test/shared/icell8-test/72618_HCT116_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_HCT116_L001_R2_001.fastq" "test/shared/icell8-test/72618_HCT116_L002_R2_001.fastq" \

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

 --jobmode "sge"

if [ -f test/shared/icell8-test/72618_HCT116_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_HCT116_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/HCT116_S1_L001_R2_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_HCT116_S1_L001_R2_001.fastq

fi

if [ -d test-icell8-HCT116-1-lane ];then

    rm -rf test-icell8-HCT116-1-lane

fi

bash launch_universc.sh --id "test-icell8-72618_HCT116-1-lane" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_HCT116_L001_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_HCT116_L001_R2_001.fastq" \

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

 --jobmode "sge"



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 "sge"

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

if [ -d test-icell8-KU812-1-lane ];then

    rm -rf test-icell8-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 "sge"



if [ -f test/shared/icell8-test/72618_NCI-H2452_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_NCI-H2452_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_NCI-H2452_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_NCI-H2452_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_NCI-H2452_S2_L002_R1_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_NCI-H2452_S2_L002_R1_001.fastq

fi

if [ -f test/shared/icell8-test/72618_NCI-H2452_S2_L002_R2_001.fastq ]; then

    rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_NCI-H2452_S2_L002_R2_001.fastq

fi

if [ -d test-icell8-72618-NCI-H2452-2-lanes ];then

    rm -rf test-icell8-72618-NCI-H2452-2-lanes

fi

bash launch_universc.sh --id "test-icell8-72618_NCI-H2452-2-lanes" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_NCI-H2452_L001_R1_001.fastq" "test/shared/icell8-test/72618_NCI-H2452_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_NCI-H2452_L001_R2_001.fastq" "test/shared/icell8-test/72618_NCI-H2452_L002_R2_001.fastq" \

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

 --jobmode "sge"

if [ -f test/shared/icell8-test/72618_NCI-H2452_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_NCI-H2452_S1_L001_R1_001.fastq

fi

if [ -f test/shared/icell8-test/NCI-H2452_S1_L001_R2_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_NCI-H2452_S1_L001_R2_001.fastq

fi

if [ -d test-icell8-NCI-H2452-1-lane ];then

    rm -rf test-icell8-NCI-H2452-1-lane

fi

bash launch_universc.sh --id "test-icell8-72618_NCI-H2452-1-lane" --technology "iCell8" \

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

 --read1 "test/shared/icell8-test/72618_NCI-H2452_L001_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_NCI-H2452_L001_R2_001.fastq" \

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

 --jobmode "sge"

test/run_tests_mappa.sh

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Original line number Original line Diff line number Diff line 
#!/bin/bash



# run tests in home directory (writeable)

cd ~



## test icell8 data

# unzip input data

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" \

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

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