call tests separately

sut:

  build: .

  command: echo "build complete"

  command: echo "build complete" && bash test/test_call.sh

test:

test_10x:

  build: .

  command: bash run_tests.sh

  command: bash test/run_tests_10x.sh

test_dropseq:

  build: .

  command: bash test/run_tests_dropseq.sh

test_icell8:

  build: .

  command: bash test/run_tests_icell8.sh

# run tests in home directory (writeable)

cd ~

## check cellranger installed

cellranger count ---version

## check convert is installed

bash /universc/launch_universc.sh -v

# reset barcodes for test

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

#!/bin/bash

# run tests in home directory (writeable)

cd ~

# reset barcodes for test

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

## test 10x data

# unzip input data

if [[ ! -f /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then

    gzip /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python/cellranger/barcodes/3M-february-2018.txt

fi

# test cellranger call

cellranger testrun --id="tiny-test"

# unzip input data

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

gunzip -fk /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python/cellranger/barcodes/3M-february-2018.txt.gz 

# test cellranger call

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

 --fastqs="/cellranger-3.0.2.9001/cellranger-tiny-fastq/3.0.0/" --sample="tinygex" \

 --transcriptome="/cellranger-3.0.2.9001/cellranger-tiny-ref/3.0.0"

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

 --fastqs="/cellranger-3.0.2.9001/cellranger-tiny-fastq/1.2.0/" --sample="tinygex" \

 --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-v3" --technology "10x" \

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

 --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"

# compress all input files

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

#!/bin/bash

# run tests in home directory (writeable)

cd ~

## test drop-seq data

# unzip input data

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

# test manual setup

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

# call on dropseq with files

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" 

# compress all input files

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

#!/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