Skill Claude CodeCodex
Reusable infrastructure for invoking Claude (via anthropics/claude-code-action) on Google Vertex AI from GitHub Actions workflows in this repo. Authentication is via Workload Identity Federation — no long-lived secrets.
Skill Claude CodeCodex
Guidance for scanning, triaging, and mitigating container image vulnerabilities in the viral-ngs Docker image hierarchy.
Skill Claude CodeCodex
Use dsub to run one-off compute jobs on Google Cloud when your analysis requires more compute/memory than the local environment, or needs specific Docker images that are impractical to run locally.
Skill Claude CodeCodex
End-to-end regression testing for assembly pipeline changes against Terra submissions.
Instructions file GitHub Copilot
Instructions for broadinstitute/viral-ngs, covering copilot instructions, quick reference, running tests and key files.
Instructions file CodexOpenCode
Instructions for broadinstitute/viral-ngs, covering agents.md, development environment, docker-centric development, development workflow and running tests.
Instructions file
Instructions for broadinstitute/viral-ngs, covering claude.md, quick reference, running tests and key files.
Instructions file
Instructions for broadinstitute/fiss-mcp, covering terra.bio mcp server, project purpose, technical approach, key design decisions and read-only safety mode.
Skill Claude CodeCodex
Debug failed Terra/Cromwell workflow submissions. Use when analyzing failed submissions, identifying error patterns, or troubleshooting infrastructure issues like docker pull failures, preemption, or OOM.
Skill Claude CodeCodex
Extract specific data from Cromwell workflow metadata efficiently. Use when you need task outputs, runtime attributes, or specific fields without loading full 100K+ token metadata.
Skill Claude CodeCodex
Prevent LLM context exhaustion when working with large Terra data. Use with scattered workflows (50+ shards), large data tables (100+ entities), or verbose metadata.
Skill Claude CodeCodex
Navigate and debug WDL subworkflows in Terra. Use when a workflow calls nested subworkflows and you need to find subworkflow IDs or debug nested executions.
Skill Claude CodeCodex
Submit WDL workflows to Terra safely. Use before launching workflows to verify configuration, validate inputs, and choose between single-entity and batch processing.