[jaempawi]

Polish of the xQTL protocol site and module notebooks.

Workflow builder

• Add LeafCutter2 splicing calling and QTL summary-statistics fine-mapping and TWAS weights (qtl_rss_analysis)
• Remove retired entries: GRM, ld_reference_generation, METAL_pipeline and the pseudobulk QC modules
• SuSiE-enloc notes point to the current mnm_regression and rss_analysis notebooks
• scEEMS Prediction available (model path .cbm); joint fine-mapping wording; main page heading, larger buttons, form first on phones
• LeafCutter2 page added to the site menu

Links and citations

• Fix moved notebook links (code/ paths now under code/SoS/), GTEx, 3D Genome and NIAGADS links; csg.yml link points to the SoS host setup guide
• Schmitt et al. 2017 corrected to 2016; Dai et al. 2025 corrected to Buen Abad Najar et al. 2025
• Links to private lab repositories on site pages say "(lab access only)"
• Home page: plain intro, NIAGADS as plain text, in-site Environment Setup link; README points to the reference-data PDF on Synapse

Writing

• No em dashes; 64 spaced hyphens used as dashes rewritten; US spelling; hyphenated fine-mapping; headings without colons; typo fixes
• logo_alt added in myst.yml

Checks

• tests/scripts/test_documented_command_paths.py and test_website_sources.py: 355 passed
• All changed notebooks are valid JSON; only markdown cells changed, apart from two code comments respelled (no code logic or outputs)
• xqtl_protocol_workflow_builder.html regenerates identically from the notebook with website/build_support.py
• Not yet run here: a MyST site build; please check the preview