fixtures: add funcprofiler and funcprofiler_upstream examples#337
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Adds two .mmd fixtures for the nf-core/funcprofiler pipeline: - examples/funcprofiler_upstream.mmd - the upstream pipeline as it actually renders, intended as a canonical bad-case stress test - examples/funcprofiler.mmd - a simplified variant Both fixtures currently exhibit layout defects under the current engine: - funcprofiler.mmd: inter-section trunk-Y kink (profiling -> reporting, 3px delta), qc line crosses non-consumer 'merge' marker - funcprofiler_upstream.mmd: humann3 junction routing nearly horizontal, tracked by validators in #252 Held back from the main docs gallery (#239) until the underlying engine issues are addressed; this PR lands the fixtures so the validators work and engine fixes can iterate against them.
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Updated nf-core/rnaseq fixture matching the upstream pipeline more closely: adds ribodetector, fastqc_filtered, featurecounts, sylph stations and a bowtie2_salmon line. Currently exhibits two engine-side issues that need follow-up: 1. test_auto_y_spacing_fits_content fails - hisat2_align and bowtie2_align stack at gap=10px in genome_align section (need 40px for caption clearance). 2. Visual z-order divergence between fan-out (left of sortmerna/ribodetector/bbsplit) and fan-in (right) - the ribodetector loop is on top in the descent but the sortmerna loop sits on top in the ascent. Held back from the gallery PR #239 until these are resolved; same engine-needs-work bucket as the funcprofiler fixtures in this PR.
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These need engine-side follow-up work: - funcprofiler.mmd: profiling->reporting trunk-Y kink, qc-crosses-merge - funcprofiler_upstream.mmd: humann3 junction nearly horizontal - rnaseq_auto.mmd (expanded): hisat2/bowtie2 stacking under y_spacing threshold, ascend-vs-descend z-order mismatch around bbsplit/sortmerna/ribodetector fan Moved to PR #337. Restored examples/rnaseq_auto.mmd to main's version so this PR (docs gallery + hlatyping logo path + gallery script infrastructure) lands without an engine block.
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* docs: add nf-core Pipelines page with renders for all adopted pipelines New dedicated docs page showcasing real-world nf-core/sanger-tol pipelines using nf-metro: rnaseq, epitopeprediction, hlatyping, variantprioritization, variantbenchmarking, genomeassembly, and funcprofiler. Removes pipeline-specific entries (genomeassembly, variantprioritization) from the layout gallery, keeping it focused on layout patterns. Adds funcprofiler.mmd from nf-core/funcprofiler dev branch. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * fix: use explicit .md paths in cross-page links to silence mkdocs warnings Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * docs: sync rnaseq and hlatyping examples with upstream repos Update rnaseq_auto.mmd from nf-core/rnaseq master (adds bowtie2_salmon line, ribodetector, tximport/SummarizedExperiment, file icons, explicit port directives, and section directions). Update hlatyping.mmd from nf-core/hlatyping dev (different hidden station routing with merge junction pattern, updated logo path). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * docs: add funcprofiler upstream and simplified variants, debug renders Add funcprofiler_upstream.mmd (original 11-line topology from nf-core) and simplified funcprofiler.mmd (3-line version). Both rendered on the pipelines page. Pipeline renders use debug mode for ongoing review. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * Split out funcprofiler + rnaseq_auto fixture changes These need engine-side follow-up work: - funcprofiler.mmd: profiling->reporting trunk-Y kink, qc-crosses-merge - funcprofiler_upstream.mmd: humann3 junction nearly horizontal - rnaseq_auto.mmd (expanded): hisat2/bowtie2 stacking under y_spacing threshold, ascend-vs-descend z-order mismatch around bbsplit/sortmerna/ribodetector fan Moved to PR #337. Restored examples/rnaseq_auto.mmd to main's version so this PR (docs gallery + hlatyping logo path + gallery script infrastructure) lands without an engine block. * Regenerate docs/pipelines/index.md from build_gallery.py The PR initially committed a hand-edited version of the file; CI's render-diff job runs the gallery script, which rewrites the file from its PIPELINE_ENTRIES list, and the resulting diff blocked the base branch checkout step. Committing the script's output verbatim so the file matches what CI regenerates and the workflow's base-branch checkout can proceed. * chore: stop committing build_gallery.py-generated docs/pipelines/index.md The file is regenerated from PIPELINE_ENTRIES by scripts/build_gallery.py on every invocation, including the docs build in CI. Committing it kept us tied to a stale snapshot that diverged from the script's output and broke the render-diff workflow's base-branch checkout step. Add to .gitignore alongside docs/gallery/index.md (which has always been generated and never committed). CI and the mkdocs site builder will regenerate the file from the script on demand. * Remove funcprofiler fixtures (resurrected by accident; they live in #337) --------- Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Adds two .mmd fixtures for the nf-core/funcprofiler pipeline so the validators in #252 (and follow-up engine work) have a target.
These fixtures currently fail layout invariants from #326 and validators from #252. Held back from the docs gallery (#239) until the engine work to lay them out cleanly lands.
DO NOT MERGE
This PR is intentionally draft. Land only after the underlying engine fixes resolve the documented defects.