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Feat/pipeline selector landing page - #1402

Merged

danielnachun merged 29 commits into

StatFunGen:mainfrom

jaempawi:feat/pipeline-selector-landing-page

Aug 13, 2026

Commits on Aug 4, 2026
- docs: make self-referential notebook paths repo-relative
  jaempawi
  committed
  aed08f3
Commits on Aug 5, 2026
- feat: interactive pipeline selector landing page
  jaempawi
  committed
  384819a
- docs(snakemake): drop py_compile refs to Python workers removed in #1393
  jaempawi
  committed
  70064f2
- revert: leave graveyard notebooks untouched
  jaempawi
  committed
  6a07d0d
- docs: fix doubled pipeline/pipeline/ path in bulk_expression_commands
  jaempawi
  committed
  dd67775
- chore: move landing page under code/SoS so the site build stages it
  jaempawi
  committed
  10d972b
- feat(website): add pipeline selector as a book page
  jaempawi
  committed
  669031d
- docs(getting-started): pixi-only install, in-repo example data
  jaempawi
  committed
  920a5df
- docs(getting-started): add 8-bit three-step gif
  Anak Empawi
  committed
  8446db1
- fix(website): wrap selector HTML in a raw directive so MyST leaves the JS alone
  Anak Empawi
  committed
  6d862a7
- docs(website): retitle selector page "Which pipelines do I need?"
  Anak Empawi
  committed
  7205e02
- docs(modules): restore Input/Output sections dropped by the narrative-sync PRs
  Anak Empawi
  committed
  23f6dd7
- docs(modules): restore column and format descriptions removed by the narrative-sync PRs
  Anak Empawi
  committed
  74f901e
- docs(twas_ctwas): add Overview with cTWAS citation, Input, worked example, command interface
  Anak Empawi
  committed
  8825b16
- fix(notebooks): match cell id fields to each notebook nbformat version
  Anak Empawi
  committed
  f9b6295
- docs(rss_analysis): add Overview with SuSiE-RSS citation and a fixtures-based worked example
  Anak Empawi
  committed
  a96ee0c
- docs(mnm_regression): add Overview with SuSiE and mvSuSiE citations, tested worked example
  Anak Empawi
  committed
  2525b6d
- docs(modules): add Overview and tested worked examples to qtl_association_postprocessing and gene_annotation
  Anak Empawi
  committed
  4948dd5
- docs(colocboost): add Overview with ColocBoost citation and tested worked example
  Anak Empawi
  committed
  3a49eb8
- docs(modules): add Overview to PCA, apa_calling and bulk_expression_QC
  Anak Empawi
  committed
  e35153f
Commits on Aug 8, 2026
- fix CTWAS test
  danielnachun
  committed
  0a2371a
Commits on Aug 12, 2026
- Standardize module notebook documentation
  Anak Empawi
  committed
  949f418
- Merge remote-tracking branch 'origin/main' into feat/pipeline-selector-landing-page
  Anak Empawi
  committed
  9bcc737
- Keep module format specification local
  Anak Empawi
  committed
  73ac5a6
- Complete module narrative audit
  Anak Empawi
  committed
  132ef4f
- Merge remote-tracking branch 'fork/feat/pipeline-selector-landing-page' into feat/pipeline-selector-landing-page
  Anak Empawi
  committed
  763a6d6
- Standardize mini-protocols and vignettes
  Anak Empawi
  committed
  c6ac427
- fix test failures
  danielnachun
  committed
  5a58e22
Commits on Aug 13, 2026
- fix more tests
  danielnachun
  committed
  7a38abf

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Feat/pipeline selector landing page - #1402

Feat/pipeline selector landing page#1402
danielnachun merged 29 commits into
StatFunGen:mainfrom
jaempawi:feat/pipeline-selector-landing-page

Commits on Aug 4, 2026

docs: make self-referential notebook paths repo-relative

Commits on Aug 5, 2026

feat: interactive pipeline selector landing page

docs(snakemake): drop py_compile refs to Python workers removed in #1393

revert: leave graveyard notebooks untouched

docs: fix doubled pipeline/pipeline/ path in bulk_expression_commands

chore: move landing page under code/SoS so the site build stages it

feat(website): add pipeline selector as a book page

docs(getting-started): pixi-only install, in-repo example data

docs(getting-started): add 8-bit three-step gif

fix(website): wrap selector HTML in a raw directive so MyST leaves the JS alone

docs(website): retitle selector page "Which pipelines do I need?"

docs(modules): restore Input/Output sections dropped by the narrative-sync PRs

docs(modules): restore column and format descriptions removed by the narrative-sync PRs

docs(twas_ctwas): add Overview with cTWAS citation, Input, worked example, command interface

fix(notebooks): match cell id fields to each notebook nbformat version

docs(rss_analysis): add Overview with SuSiE-RSS citation and a fixtures-based worked example

docs(mnm_regression): add Overview with SuSiE and mvSuSiE citations, tested worked example

docs(modules): add Overview and tested worked examples to qtl_association_postprocessing and gene_annotation

docs(colocboost): add Overview with ColocBoost citation and tested worked example

docs(modules): add Overview to PCA, apa_calling and bulk_expression_QC

Commits on Aug 8, 2026

fix CTWAS test

Commits on Aug 12, 2026

Standardize module notebook documentation

Merge remote-tracking branch 'origin/main' into feat/pipeline-selector-landing-page

Keep module format specification local

Complete module narrative audit

Merge remote-tracking branch 'fork/feat/pipeline-selector-landing-page' into feat/pipeline-selector-landing-page

Standardize mini-protocols and vignettes

fix test failures

Commits on Aug 13, 2026

fix more tests