In this project a new domain for APE (Automated Pipeline Explorer) was created based on the metagenomics pipeline MetaCascabel. It consists of an ontology, tool description, constraints and configuration file. Using APE, variants of the metacascabel pipeline can be generated. For each generated workflow, an executable script as well as a graphical representation is being created.
APE:
https://github.com/sanctuuary/APE
MetaCascabel:
https://github.com/AlejandroAb/Meta-CASCABEL
To generate workflows, you can edit desired input and output in the config file. Use the following command to start the workflow composition:
java -jar APE-2.5.2-executable.jar ./config.json
To add specific preferences for your workflow you can add to the constraints.json file. For constraint templates see: https://ape-framework.readthedocs.io/en/latest/docs/specifications/constraints.html