Skip to content

docs(site): add cellagdiffexp docs, demote tucca-rna-seq to legacy - #15

Open
benjibromberg wants to merge 2 commits into
mainfrom
feat/cellagdiffexp-docs
Open

docs(site): add cellagdiffexp docs, demote tucca-rna-seq to legacy#15
benjibromberg wants to merge 2 commits into
mainfrom
feat/cellagdiffexp-docs

Conversation

@benjibromberg

Copy link
Copy Markdown
Member

Adds a documentation section for the new cellagdiffexp Nextflow pipeline and makes it the featured pipeline on the site, demoting the older Snakemake tucca-rna-seq to a kept-but-legacy status (its docs and URLs stay intact).

What changed

New docs section site/src/content/docs/cellagdiffexp/ (4 pages, ported from the pipeline repo's canonical docs, adapted to Starlight):

  • introduction.mdx — what it is (downstream of nf-core/rnaseq, matrix-in), feature overview, successor note.
  • usage.mdx — inputs, contrasts (simple + advanced/interaction/DREAM), annotation + enrichment params, SPIA (native + KO routes), DE options, running examples (test/test_chicken/test_pig).
  • output.mdx — every output directory.
  • architecture.mdx — the Lean B owned-vs-reused boundary, data-flow diagram, ADR summaries, per-phase history, verification strategy.

Navigation (cellagdiffexp is now primary; tucca-rna-seq kept as legacy):

  • Sidebar (astro.config.mjs): new cellagdiffexp group; tucca-rna-seq relabeled (legacy) and collapsed.
  • Navbar (SiteTitle.astro): the Docs dropdown now points at cellagdiffexp (with a legacy link kept); cellagdiffexp added to the Projects dropdown and the mobile menu.
  • Landing page (index.mdx): new cellagdiffexp project card; tucca-rna-seq card marked legacy.
  • tucca-rna-seq/introduction.mdx: the roadmap note strengthened into a "Frozen: superseded by cellagdiffexp" banner.

Notes

  • Strategy: deprecate + demote (not delete). All 18 tucca-rna-seq pages and their public URLs are preserved (no 404s, useful Tufts HPC guides kept); it is just no longer the featured pipeline.
  • Build verified locally: pnpm build clean on node 22 (all 30 pages, including the 4 new ones; sidebar/nav slugs resolve). No em dashes, no AI-tell vocabulary.
  • Deploys to the live site on merge to main, so left unmerged for your review.

🤖 Generated with Claude Code

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant