Computational pipelines have become ubiquitous in bioinformatics, with an increasing need for sharing them among researchers in portable formats like the Common Workflow Language (CWL) standard.
Galaxy has been involved in the development of the CWL standard from the start, and native support for CWL in Galaxy has been developed in a fork of the Galaxy codebase created by John Chilton.
The first four European BioHackathons allowed several different contributors to work together on this project and discuss with the wider communities. This resulted in major progress in the CWL support in Galaxy, and in large portions of the CWL branch of Galaxy making their way into the core repository. In particular, in the 2021 edition we refactored the code in the fork going from 1,245 files (+241,593 lines of code) to just 92 files (+4,361 lines).
An initial Galaxy implementation of a major feature of the v1.2 version of the CWL specification was developed during the 2020 BioHackathon Europe: conditional execution of a workflow step. We plan to finish this work and merge the pull request ( common-workflow-lab/galaxy#123 ) in the Galaxy fork.
Other goals for the 2022 BioHackathon will be to fix the 12 remaining required CWL 1.2 conformance tests, work on the other open issues ( tracked at https://github.com/common-workflow-language/galaxy/issues ), and continue the merge of the separate CWL branch into the upstream Galaxy repository.
Compute Platfrom Galaxy Interoperability Platform Tools Platform
Project Number: 28
Michael R. Crusoe
- Complete the implementation of CWL 1.2 conditionals and workflow default files in Galaxy
- Support for ResourceRequirement to specify computational resources needed by a tool
- Mapping of data ontologies to Galaxy datatypes for better mixing of CWL and Galaxy pipelines
- Fix remaining CWL conformance tests
- Advance the merge of the separate branch into the upstream Galaxy repository to be part of future Galaxy releases
Software developers with either Python or Web Frontend development skills (especially JavaScript/Vue.js), with or without an initial experience of development in Galaxy and/or CWL.
Number of expected hacking days: 4