docs(site): add cellagdiffexp docs, demote tucca-rna-seq to legacy - #15
Open
benjibromberg wants to merge 2 commits into
Open
docs(site): add cellagdiffexp docs, demote tucca-rna-seq to legacy#15benjibromberg wants to merge 2 commits into
benjibromberg wants to merge 2 commits into
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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):
astro.config.mjs): newcellagdiffexpgroup;tucca-rna-seqrelabeled(legacy)and collapsed.SiteTitle.astro): the Docs dropdown now points at cellagdiffexp (with a legacy link kept); cellagdiffexp added to the Projects dropdown and the mobile menu.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
pnpm buildclean on node 22 (all 30 pages, including the 4 new ones; sidebar/nav slugs resolve). No em dashes, no AI-tell vocabulary.main, so left unmerged for your review.🤖 Generated with Claude Code