Add Bio-Pype LSP extension to Zed - #7004
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We require contributors to sign our Contributor License Agreement, and we don't have @ffavero on file. You can sign our CLA at https://zed.dev/cla. Once you've signed, post a comment here that says '@cla-bot check'. |
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We require contributors to sign our Contributor License Agreement, and we don't have @ffavero on file. You can sign our CLA at https://zed.dev/cla. Once you've signed, post a comment here that says '@cla-bot check'. |
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Bio_pype is a framework for building computing workflows, primarily used in bioinformatics. It consists of three core structural modules that connect and execute tasks:
Profiles: YAML definitions of reference files (genomes, annotations) and programs, specifying versions and execution contexts (Docker, Singularity, environment modules, etc.)
Snippets: Markdown files describing individual tasks, leveraging profiles to ensure correct environment setup and appropriate annotation file versions
Pipelines: YAML files defining a directed acyclic graph (DAG) that orchestrates snippet execution in the proper order
This Zed extension leverages bio_pype's internal validation framework and LSP server to provide IDE support for snippet markdown, pipeline, and profile YAML files. It includes:
Autocompletion
Hover information
Diagnostics feedback