Foundation: scaffolding, docs, and prek validation harness#5
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edmundmiller wants to merge 4 commits into
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Foundation: scaffolding, docs, and prek validation harness#5edmundmiller wants to merge 4 commits into
edmundmiller wants to merge 4 commits into
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Branded README (logo, badges, repo rules) with skills table + install instructions, AGENTS.md table of contents, and docs/ (ARCHITECTURE, CONTRIBUTING). Repo references point at nf-core/agents. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
prek.toml hooks (SKILL.md frontmatter, nf-core lint wrappers, schema checks), their scripts under scripts/prek-hooks/, the harness unit tests, and the GitHub Actions workflow that runs prek. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This was referenced Jun 16, 2026
scripts/agent_hooks/ (provider-agnostic phase/stop runner with Claude, Codex, Cursor, generic adapters) lives here because the prek harness tests in tests/prek-hooks/ exercise it. Provider docs ship separately. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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The harness test hook (tests/prek-hooks/run-tests.py) and the nf-core lint wrappers run via a `uv run --script` shebang, so the runner needs uv on PATH or prek fails to spawn the hook (os error 2). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Foundation PR for porting edmundmiller/nf-core-skills into
nf-core/agents, per the #agents Slack thread.This is the keystone of a focused, per-skill PR series. Merge this first so the per-skill PRs are validated by CI.
Included
README.md— keeps nf-core branding (logo, badges, repository rules); adds the skills table + install instructions for Claude Code, Codex CLI, OpenCode, Cursor.AGENTS.md— table of contents for agents working in this repo.docs/ARCHITECTURE.md,docs/CONTRIBUTING.md.prek.toml+scripts/prek-hooks/+tests/prek-hooks/— SKILL.md frontmatter validation, nf-core lint wrappers, schema checks..github/workflows/prek.yml— runs prek in CI..markdownlint.json.Series (each off
main, disjoint files)nf-core-pipelineskillnf-core-lintskillnf-core-moduleskillnf-core-containersskillscripts/agent_hooks/+ docs)AGENTS.md/docslink to files arriving in later PRs in the series; links resolve as the series merges. Supersedes the content split in #3/#4.🤖 Generated with Claude Code