ga4gh-skills

Write, understand, and structure Workflow Description Language (WDL) files. Use this skill whenever the user is writing or editing WDL tasks, workflows. Trigger on phrases like "cromwell", "miniwdl", "Terra workflow", "WDL runtime block", or any request to define bioinformatics or data-processing pipelines using WDL syntax. Also trigger when the user pastes WDL code and asks for help, review, or explanation.

Install and use Refgenie CLI to download and manage reference genomes locally. Trigger this skill whenever a user wants to install Refgenie, download reference genome assets, manage a local Refgenie database, configure Refgenie settings, or perform CLI-based genome management tasks. Use this for hands-on genome provisioning workflows.

Use the Refgenie MCP (Model Context Protocol) server to search for and discover reference genome names and assets. Trigger this skill whenever a user wants to search for available reference genomes, browse genome collections, look up specific genome builds, or discover what reference assets are available without installing Refgenie locally. This is useful for exploratory queries, checking what references exist, or integrating genome discovery into workflows.

Install and use Refget CLI tools to download, query, and manage reference sequences locally. Trigger this skill whenever a user wants to install Refget (Python or Rust versions), download sequences by hash, query local sequence databases, validate sequence checksums, set up local Refget servers, or perform sequence retrieval workflows. Use for hands-on sequence access and validation.

Use the Refget MCP (Model Context Protocol) server to search and access reference sequences by hash. Trigger this skill whenever a user wants to search for sequence collections, look up sequences by identifier, verify sequence checksums, browse Refget collections, or integrate sequence access into workflows. Ideal for discovering what sequences are available without local installation.

Coordinate use of GA4GH reference genome and sequence tools (Refgenie, Refget, and their MCP servers). Trigger this skill whenever a user is working with reference data management, genome provisioning, sequence access, or needs guidance on which tool to use. Use this to select the right tool combination for bioinformatics workflows.

Validate, lint, and fix WDL files using womtool, miniwdl check, and/or sprocket. Use this skill whenever the user wants to check WDL syntax, understand or fix lint warnings, suppress specific rules, interpret tool error output, set up CI validation, or run any of: womtool validate, miniwdl check, sprocket check, sprocket lint, or sprocket format. Also trigger when the user pastes tool output containing WDL errors or warnings and asks for help understanding or fixing them.