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BEDboss insert

Bedboss supports inserting and running all pipelines using a single command: bedboss insert.

To run bedboss insert you need to have few things set up:
0) Installed bedboss dependencies. See bedboss dependencies for more information
1) Created config file with all the necessary information. See bedboss config for more information
2) PEP project with all the necessary information. Project can be stored locally or on PEPhub
Before running pipeline PEP should be validated using eido or pephub schema. Bedboss insert schema: bedboss insert schema
3) Provide path to output directory

Additional information can be found in the bedboss insert documentation.

Example PEP:

Example run:

When we have all the necessary information we can run the pipeline:

bedboss insert --bedbase-config bedboss_config.yaml --pep khoroshevskyi/example --output-folder ./bedboss_output