Make rss_analysis.ipynb the GWAS RSS fine-mapping workflow

code/SoS/mnm_analysis/summary_stats_finemapping_vignette.ipynb

@@ -81,7 +81,7 @@
    "source": [
     "# Build per-(study, LD-block) GwasSumStats, run SuSiE-RSS fine-mapping,\n",
     "# and render PIP plots end-to-end with the new pecotmr-integration pipeline:\n",
-    "sos run pipeline/gwas_rss_fine_mapping.ipynb \\\n",
+    "sos run pipeline/rss_analysis.ipynb \\\n",
     "    generate_gwas_sumstats+gwas_fine_mapping+gwas_rss_plot \\\n",
     "    --cwd output/rss_analysis \\\n",
     "    --gwas-meta data/mnm_regression/gwas_meta_data.txt \\\n",

code/SoS/pecotmr_integration/fine_mapping_postprocessing.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "## Description\n",
     "\n",
-    "Postprocessing utilities for the S4 `QtlFineMappingResult` / `GwasFineMappingResult` RDSes produced by `fine_mapping.ipynb`, `multivariate_fine_mapping.ipynb`, `functional_fine_mapping.ipynb`, or `gwas_rss_fine_mapping.ipynb`. Replaces the legacy `mnm_analysis/mnm_postprocessing.ipynb` (which consumed the older list-shaped RDS layout).\n",
+    "Postprocessing utilities for the S4 `QtlFineMappingResult` / `GwasFineMappingResult` RDSes produced by `fine_mapping.ipynb`, `multivariate_fine_mapping.ipynb`, `functional_fine_mapping.ipynb`, or `rss_analysis.ipynb`. Replaces the legacy `mnm_analysis/mnm_postprocessing.ipynb` (which consumed the older list-shaped RDS layout).\n",
     "\n",
     "All steps consume FMR RDSes through the pecotmr S4 accessor surface (`getPip`, `getCs`, `getTopLoci`, `getMarginalEffects`, `getVariantIds`) so they work uniformly for QTL and GWAS outputs.\n",
     "\n",

code/script/pecotmr_integration/fine_mapping_pip_plot.R

@@ -4,7 +4,7 @@
 # Render a per-region PIP landscape plot from a QtlFineMappingResult or
 # GwasFineMappingResult RDS (output of fine_mapping.ipynb /
 # multivariate_fine_mapping.ipynb / functional_fine_mapping.ipynb /
-# gwas_rss_fine_mapping.ipynb). One PNG per input RDS, one facet panel
+# rss_analysis.ipynb). One PNG per input RDS, one facet panel
 # per row in the FMR.
 #
 # Inputs:

code/script/pecotmr_integration/gwas_rss_manifest.R

@@ -1,7 +1,7 @@
 #!/usr/bin/env Rscript
 # gwas_rss_manifest.R
 #
-# Resolve `gwas_rss_fine_mapping.ipynb`'s per-study GWAS sources (a
+# Resolve `rss_analysis.ipynb`'s per-study GWAS sources (a
 # --gwas-meta TSV and/or --gwas-tsv-list STUDY=PATH items) together with
 # its region inputs (a --region-list BED-ish file and/or --regions
 # chr:start-end strings) into a single per-job manifest TSV. One row per