claude-agent-workflow

name	claude-agent-workflow
description	Add or update claude.yml workflow.
user-invocable	true
allowed-tools	["Read","Edit","Write","Bash"]

claude-agent-workflow

Sets up or edits the @claude agent GitHub Actions workflow (.github/workflows/claude.yml or .github/workflows/claude-bot.yml), which delegates to the reusable claude.yml workflow from Morrison-Lab/gha. For the read-only PR review workflow, use claude-review-workflow.

Path: .github/workflows/claude.yml (or .github/workflows/claude-bot.yml)

Standard caller stub

name: Claude Code

on:
  issue_comment:
    types: [created]
  pull_request_review_comment:
    types: [created]
  # Summon the agent explicitly: assign the issue (requires mention in body/title),
  # or mention the bot in a comment. Deliberately not `issues: opened` to avoid
  # dispatching on issues that merely discuss the bot.
  issues:
    types: [assigned]
  pull_request_review:
    types: [submitted]

jobs:
  claude:
    permissions:
      contents: write
      pull-requests: write
      issues: write
      id-token: write
      actions: write
    uses: Morrison-Lab/gha/.github/workflows/claude.yml@v2
    secrets: inherit
    with:
      setup-r: false
      eager-pr: true
      review-workflow-file: claude-review.yml

Load-bearing pieces (managed by Morrison-Lab/gha)

By delegating to Morrison-Lab/gha/.github/workflows/claude.yml@v2, the consumer repo automatically inherits:

1. Bot-actor filtering: Evaluates mention triggers (@claude) on comments, reviews, and assigned issues while filtering out bot-generated loops.
2. Concurrency serialization: Per-issue/PR concurrency with cancel-in-progress: false to avoid clobbering concurrent in-flight agent pushes.
3. Late-comment polling: Scans for comments arriving during execution so long-running sessions drain multi-comment bursts.
4. Post-push review triggering: Captures head SHAs before and after execution; if changes were pushed, automatically requests review and dispatches the review workflow.
5. Tool permission sandboxing: Restricts allowed CLI tools (gh read commands, git, build tools) and enforces secure WebFetch domain allowlisting.
6. Threaded inline replies: Automatically posts responses as threaded inline replies when triggered by pull request review comments.
7. Environment and secret propagation: Handles private submodules (SUBMODULES_TOKEN) and optional domain tokens (EPI202_TOKEN).

Inputs and customization

• setup-r: Initialize R toolchain and renv package cache (true for R packages / Quarto R repos).
• eager-pr: Open a draft PR up front when claiming an issue (true by default).
• review-workflow-file: Name of the companion review workflow file (e.g. claude-review.yml or claude-code-review.yml).
• use-ai-config: Automatically load ai-config agent instructions (defaults to true, set false for Morrison-Lab/ai-config itself).
• apt-packages / pip-packages: Additional build or analysis packages.

Setting up in a new repo

1. Confirm CLAUDE_CODE_OAUTH_TOKEN secret exists in repo/org secrets (gh secret list).
2. Add the caller stub at .github/workflows/claude.yml.
3. Ensure required permissions (contents: write, pull-requests: write, issues: write, id-token: write, actions: write) are declared on the caller job.
4. Configure appropriate inputs (setup-r, review-workflow-file, etc.).

Relationship to other skills

• claude-review-workflow — Companion skill for the automated PR review workflow.
• upgrade-to-gha — Migration guidelines for upgrading standalone workflows to Morrison-Lab/gha.
• config-ai — Router for AI workflow capability requests.