Feat/pipeline selector landing page - #1402
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Documented sos run examples pointed at personal checkouts (~/codes/xqtl-protocol/, /home/hs3163/GIT/xqtl-protocol/, ~/GIT/xqtl-protocol/), so they could only work for their author. Replaced the prefixes with plain pipeline/ paths. No other path classes touched.
Answers "which pipelines do I need" from a few questions about the user data, then lists the applicable pipelines with inputs, outputs and commands. High-dimensional Regression is organised by data level (individual vs summary statistics), with fine-mapping and TWAS weights as products of the same run per Gao. RSS TWAS weights and scEEMS Prediction are marked as not yet wired into SoS.
…atFunGen#1393 genotype_formatting.py, bulk_expression_normalization.py and RNA_calling.py were ported to R and deleted, so the README verification snippet failed at the first step.
MRAID_QTL and polyfun are deprecated; no need to rewrite their paths.
Three references read pipeline/pipeline/reference_data.ipynb; pipelines are run as pipeline/<name>.ipynb from the repo root.
build_flat_book.py collects *.ipynb from code/SoS as pages and copies other files there as assets; a file at the repo root is not staged.
Jupyter Book only builds documents listed in _toc.yml (only_build_toc_files: true) and cannot render a raw .html as a page, so the selector is wrapped in a notebook with the markup in a markdown cell.
Removes the conda step: pixi-setup already provides sos, jupyter and a registered sos kernel, and the old advice to conda activate sos pointed users away from the environment holding plink/samtools/tensorqtl. Fixes the installer command: piped into bash the two prompts consume nothing, so users silently got a minimal install. Download then run instead. Replaces the Synapse download with tests/fixtures/, which ships in the repo, and links the pipeline selector.
…narrative-sync PRs
…mple, command interface
…es-based worked example
…tested worked example
…tion_postprocessing and gene_annotation
…r-landing-page # Conflicts: # code/SoS/association_scan/TensorQTL/TensorQTL.ipynb # code/SoS/pecotmr_integration/twas_ctwas.ipynb # website/_toc.yml
…e' into feat/pipeline-selector-landing-page
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Summary
This PR standardizes the documentation of 42 active SoS module notebooks using a consistent structure:
It improves the method narratives, explains when each module should be run, documents command-line flags and generated files, adds representative previews, and provides runnable
sos runexamples.Small APA-calling and PCA example files are included where needed by the documentation.
Scope
code/SoS/graveyard/are excludedValidation
The branch incorporates the latest
mainand the existing cTWAS test fix. Upstream workflow changes and graveyard moves were preserved.