🚀Running Pipelines

After creating the pipeline configuration file, it is time to run it. COSAP comes with a pipeline runner currently supported by Snakemake. To create a COSAP PipelineRunner:

from cosap import PipelineRunner

runner = PipelineRunner()

You can then run the pipeline with the previously created config:

runner.run_pipeline(pipeline_config=pipeline_config)

Setting up GPU-Accelerated Pipeline Runner

COSAP supports the NVIDIA Parabricks suite for GPU accelerated tasks in several steps. Parabricks must be set up beforehand manually. To do this please follow the instructions at Parabricks Documentation.

After you set up Parabricks, you can activate it in the pipeline runner as follows:

from cosap import PipelineRunner

runner = PipelineRunner(device="gpu")