workflomics-benchmarker 0.1.0

Library used to execute workflows (in CWL) and benchmark them as part of the Workflomics ecosystem.

Workflomics Benchmarker

Library used to execute workflows (in CWL) and benchmark them as part of the Workflomics ecosystem.

Credits

The workflomics benchmarker script was developed by Nauman Ahmed as part of the containers repository, but was since migrated to its own repository (see PR #49) to be published as a stand-alone package.

Requirements

• Python 3.9+
• Poetry
• Docker or Singularity running

Installation

poetry install 

Usage

The command is used with Docker or Singularity service running. It will execute the workflow and benchmark it.

Docker

workflomics benchmark tests/data/

which is equivalent to

python src/benchmarker/workflomics.py benchmark tests/data/

The results will be stored in the ./tests/data folder.

Singularity

Finally, you can run the test with Singularity. This will require you to have Singularity installed and running, and to use the --singularity flag.

python src/benchmarker/workflomics.py benchmark tests/data/ --singularity

Testing

To run the tests, you can use the following command:

poetry run pytest -s

The tests will execute a workflow and benchmark it (require Docker running). The results will be stored in the ./tests/data folder.