Commit 87caa450 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update test jobs to ensure reuse

parent b344f972

test/run_tests_10x_local.sh

+90 −5
Original line number Diff line number Diff line
@@ -92,11 +92,13 @@ 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

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq.gz ]]; then

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

    rm -rf 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

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq.gz ]]; then

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

    rm -rf  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" \
@@ -104,6 +106,89 @@ bash launch_universc.sh --id "test-10x-v3" --technology "10x" \ 
 "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002" \

 --per-cell-data --jobmode "local" --localcores 2 --localmem 4



# call convert on 10x with multiple lanes with compressed files

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

    rm -rf test-10x-v3-zip

fi

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

    rm -rf input4cellranger_test-10x-v3-zip

fi

# unzip input data

if [[ ! -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq.gz ]]; then

    pigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001*fastq

    rm -rf  test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001*fastq

fi

if [[ ! -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq.gz ]]; then

    pigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002*fastq

    rm -rf test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002*fastq

fi

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

 --per-cell-data --jobmode "local" --localcores 2 --localmem 4



# call convert on 10x with multiple lanes with *some* compressed files

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

    rm -rf test-10x-v3-zip-mix

fi

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

    rm -rf input4cellranger_test-10x-v3-zip-mix

fi

# unzip input data

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq.gz ]]; then

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

    rm -rf  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_R1_001.fastq.gz ]]; then

    pigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002*fastq

    rm -rf  test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002*fastq

fi

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

 --per-cell-data --jobmode "local" --localcores 2 --localmem 4



# call convert on 10x with multiple lanes with *some* compressed files

if [[ -d test-10x-v3-zip-mix-2 ]]; then

    rm -rf test-10x-v3-zip-mix-2

fi

if [[ -d input4cellranger_test-10x-v3-zip-mix-2 ]]; then

    rm -rf input4cellranger_test-10x-v3-zip-mix-2

fi

# unzip input data

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq.gz ]]; then

    unpigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq.gz

    rm -rf  test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq.gz

    pigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R2_001.fastq

    rm -rf  test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R2_001.fastq

fi

if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq.gz ]]; then

    unpigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq.gz

    rm -rf  test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq.gz

    pigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq

    rm -rf  test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq

fi

bash launch_universc.sh --id "test-10x-v3-zip-mix-2" --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" \

 --per-cell-data --jobmode "local" --localcores 2 --localmem 4



# call convert on 10x with multiple lanes with *some* compressed files

if [[ -d test-10x-v3-zip-mix-3 ]]; then

    rm -rf test-10x-v3-zip-mix-3

fi

if [[ -d input4cellranger_test-10x-v3-zip-mix-3 ]]; then

    rm -rf input4cellranger_test-10x-v3-zip-mix-3

fi

bash launch_universc.sh --id "test-10x-v3-zip-mix-3" --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" \

 --per-cell-data --jobmode "local" --localcores 2 --localmem 4



# 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

test/run_tests_dropseq_local.sh

+8 −4
Original line number Diff line number Diff line
@@ -20,9 +20,13 @@ 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

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

    unpigz -f test/shared/dropseq-test/SRR1873277_Sample1_R1.fastq.gz

fi

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

    unpigz -f test/shared/dropseq-test/SRR1873277_Sample1_R2.fastq.gz

fi



# test manual setup

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

test/run_tests_icell8_local.sh

+43 −7
Original line number Diff line number Diff line
@@ -18,19 +18,47 @@ if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ 
    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

unpigz -f -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_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_S2_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_S2_L002_R2_001.fastq ]; then

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

fi

if [ -f input4cellranger_test-icell8-72618_KU812-2-lanes-non-umi ]; then

    rm -rf input4cellranger_test-icell8-72618_KU812-2-lanes-non-umi

fi

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

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

fi

bash launch_universc.sh --id "test-icell8-72618_KU812-2-lanes-non-umi" --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" \

 --per-cell-data --jobmode "local" --localcores 2 --localmem 4 --non-umi



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_S2_L002_R1_001.fastq ]; then

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

    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_S2_L002_R2_001.fastq ]; then

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

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

fi

if [ -f input4cellranger_test-icell8-72618_KU812-2-lanes ]; then

    rm -rf input4cellranger_test-icell8-72618_KU812-2-lanes

fi

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

    rm -rf test-icell8-72618_KU812-2-lanes
@@ -41,18 +69,22 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-2-lanes" --technology "iCe 
 --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" \

 --per-cell-data --jobmode "local" --localcores 2 --localmem 4



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

if [ -f test/shared/icell8-test/72618_KU812_S2_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

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

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

fi

if [ -d input4cellranger_test-icell8-72618_KU812-1-lane ]; then

    rm -rf input4cellranger_test-icell8-72618_KU812-1-lane

fi

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

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

fi
@@ -62,9 +94,13 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-1-lane" --technology "iCel 
 --read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" \

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

 --per-cell-data --jobmode "local" --localcores 2 --localmem 4



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



pigz -f -k test/shared/icell8-test/72618_KU812*fastq

rm -rf test/shared/icell8-test/72618_KU812*fastq.gz

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