CeleScope tests

Please note that these test data are only for testing whether the pipeline can run, and the data does not represent the real data quality. For testing purposes and the capacity limit of the GitHub repository, each test data contains only a few reads and may be mixed data from multiple libraries, or simulated data.

1. Get test data and scripts.

mkdir test_dir
cd test_dir
git clone https://github.com/singleron-RD/celescope_test_data.git
git clone https://github.com/singleron-RD/celescope_test_script.git

If github is blocked, an alternate repo(gitee) is available.

mkdir test_dir
cd test_dir
git clone https://gitee.com/singleron-rd/celescope_test_data.git
git clone https://gitee.com/singleron-rd/celescope_test_script.git

2. Modify arguments

• rna

celescope_test_script/rna/run_shell.sh Change --genomeDir to the human genomeDir path.

• dynaseq

celescope_test_script/dynaseq/run_shell.sh Change --genomeDir to the mouse genomeDir path.

• snp

celescope_test_script/snp/run_shell.sh Change --genomeDir to the human genomeDir path.

• capture_virus

celescope_test_data contains the EBV fasta. You can generate a EBV genomeDir by using mkref.sh under celescope_test_data/capture_virus/EBV_genome .

celescope_test_script/capture_virus/run_shell.sh Change --virus_genomeDir to the EBV genomeDir path.

3. Run pytest

• Install pytest

pip install pytest

• Run some tests

cd celescope_test_script
python -m pytest -s test_multi.py --assays tag,vdj

• Run all tests

cd celescope_test_script
python -m pytest -s test_multi.py