Foundation: README, AGENTS.md, and docs - #5
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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>
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>
mashehu
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mashehu
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waaaaaay too many files.
we want to keep this repo as slim as possible, because it will be a pain to keep in sync with the tools and docs...
Review: keep the repo slim. Remove prek.toml, scripts/ (prek + agent hooks), tests/, the prek CI workflow, and .markdownlint.json — the nf-core/tools lint wrappers are a sync burden that belongs with the tools, not here. Foundation is now just agent context: README, AGENTS.md, and docs/. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Agreed — slimmed from 36 files to 4. Dropped the whole validation harness ( Knock-on: PR #10 (docs for the now-removed agent-hook runner) is orphaned — I'll close it. PR #11 (Claude/Codex/Cursor plugin manifests + 🤖 Addressed by Claude Code |
edmundmiller
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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.Keystone of a per-skill PR series. Slimmed per review — agent context only, no tooling.
Included (4 files)
README.md— nf-core branding (logo, badges, repository rules) + skills table + install instructions (Claude Code, Codex CLI, OpenCode, Cursor).AGENTS.md— table of contents for agents working in this repo.docs/ARCHITECTURE.md,docs/CONTRIBUTING.md.Dropped per review (keep the repo slim)
The validation harness (
prek.toml,scripts/,tests/, prek CI,.markdownlint.json) was removed — the nf-core/tools lint wrappers are a sync burden that belongs with the tools, not here.Series
nf-core-pipelineskill (Addnf-core-pipelineskill #6)nf-core-lintskill (Addnf-core-lintskill #7)nf-core-moduleskill (Addnf-core-moduleskill #8)nf-core-containersskill (Addnf-core-containersskill #9)agent hook docs (Add agent hook provider docs #10)— closed (documented the removed harness)Supersedes the split in #3/#4.
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