Worker

MAcWorP's worker component fetches the scheduled workflows and executes the using the given workflow engine.

Dependencies

Conda-derivate (conda, micromamba, ...)
Java (version depends on Nextflow)
Nextflow
- Version 24.09.2-edge until https://github.com/nextflow-io/nextflow/issues/5443#issuecomment-2445609593 us fixed

Configuration is done by a command line interface, see: python -m macworp_worker --help

Parameter	Description
--nf-bin	Path to Nextflow binary
--sm-bin	Path Snakemake binary. As Snakemake is installed using the Conda, it's path can be found with `$(which snakemake)`
--macworp-url	Base-URL where the NF-Cloud instance is running: e.g. `http://localhost:3001`
--rabbitmq-url	URL for accessing the RabbitMQ-Server, e.g. `ampq://user:password@host:port/url-encoded-namespace`
--project-queue-name	Name of the RabbitMQ workflow queue
--projects-data-path	Path to the directory where user data is stored
--number-of-workers	Number of concurrent workers.
--api-user	API user for the worker, set in in config.yaml
--api-password	API password for the worker, set in in config.yaml
--verbose, -v	Verbosity. Can be used more than once. Every usage will increase thr log level.
--keep-intermediate-files	Keeps intermediate file if set. Otherwise temporary workflow folder will be deleted after workflow execution is finished
--skip-cert-verification	Skips certificate verification when talking to the API.