Commit ff301b09 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update tests for published ICELL8 data

parent 5044ea65

test/run_tests_icell8.sh

100755 → 100644
+134 −12
Original line number Diff line number Diff line
@@ -3,8 +3,8 @@ 
# run tests in home directory (writeable)

#cd ~

# run tests in universc directory

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



#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
@@ -13,9 +13,15 @@ cellrangerpath=`which cellranger` 


## test icell8 data

# unzip input data

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

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

    gunzip -f test/shared/icell8-test/*fastq.gz

#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" \
@@ -24,6 +30,9 @@ bash launch_universc.sh --id "test-icell8-default" --technology "iCell8" \ 
 --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" \
@@ -33,19 +42,36 @@ bash launch_universc.sh --id "test-icell8-custom" --technology "iCell8" \ 
 --barcodefile "test/shared/icell8-test/BarcodeList.txt" \

 --jobmode "sge"



# compress all input files

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

    gzip -f test/shared/icell8-test/*fastq

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



# 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-icell8-72618_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" \
@@ -53,25 +79,73 @@ bash launch_universc.sh --id "test-icell8-72618_A375-1-lane" --technology "iCell 
 --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"

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

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" \
@@ -79,12 +153,36 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-1-lane" --technology "iCel 
 --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" \
@@ -92,12 +190,36 @@ bash launch_universc.sh --id "test-icell8-72618_NCI-H2452-1-lane" --technology " 
 --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" \

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