diff --git a/code/SoS/mnm_analysis/mnm_methods/rss_analysis.ipynb b/code/SoS/mnm_analysis/mnm_methods/rss_analysis.ipynb
index 6fc6db24..b1f52356 100644
--- a/code/SoS/mnm_analysis/mnm_methods/rss_analysis.ipynb
+++ b/code/SoS/mnm_analysis/mnm_methods/rss_analysis.ipynb
@@ -133,59 +133,7 @@
     "kernel": "SoS"
    },
    "outputs": [],
-   "source": [
-    "[global]\n",
-    "parameter: cwd = path('output')\n",
-    "parameter: modular_script_dir = path('code/script')\n",
-    "# --- per-study GWAS inputs (use either or both) ---------------------\n",
-    "parameter: gwas_meta = path('.')\n",
-    "parameter: gwas_tsv_list = []   # list of STUDY=PATH items\n",
-    "# --- region inputs (use either or both) -----------------------------\n",
-    "parameter: region_list = path('.')\n",
-    "parameter: regions = []         # list of chr:start-end strings\n",
-    "# --- LD reference + genome ------------------------------------------\n",
-    "parameter: ld_meta = path\n",
-    "parameter: genome = 'GRCh38'\n",
-    "# --- QC knobs (forwarded to gwas_sumstats_construct.R) --------------\n",
-    "parameter: qc_method = 'none'   # none | slalom | dentist\n",
-    "parameter: impute = False\n",
-    "parameter: qc_args = ''         # JSON object spliced into summaryStatsQc()\n",
-    "parameter: maf = 0.0025         # MAF cutoff (summaryStatsQc mafCutoff); 0 disables\n",
-    "parameter: skip_regions = []    # chr:start-end window(s) whose variants are dropped (skipRegion)\n",
-    "parameter: skip_analysis_pip_cutoff = 0.025   # skip a region below this max PIP (pipCutoffToSkip); 0 disables\n",
-    "parameter: allele_flip_kriging = False   # kriging allele-flip QC: sign-flip switched z (logLR>2 & |z|>2); off by default\n",
-    "parameter: effective_n = True   # case/control: use effective sample size 4/(1/n_case+1/n_control) as N (summaryStatsQc effectiveN); False -> raw N\n",
-    "# --- fine-mapping knobs (forwarded to fine_mapping.R) ---------------\n",
-    "parameter: methods = 'susie'\n",
-    "parameter: coverage = 0.95\n",
-    "parameter: secondary_coverage = '0.7,0.5'\n",
-    "parameter: min_abs_corr = 0.8\n",
-    "parameter: median_abs_corr = ''   # empty -> off (OR-logic purity; needs pecotmr step-1)\n",
-    "parameter: pip_cutoff = 0.025\n",
-    "parameter: L = 20\n",
-    "parameter: L_greedy = 5\n",
-    "parameter: method_args = ''     # nested per-method JSON object\n",
-    "# GWAS SuSiE-RSS fine-mapping: SER fallback is ON by default (reproduces the single-panel notebook):\n",
-    "# fit finite-sample R + EB LD-mismatch SuSiE-RSS and fall back to the single-effect (SER) result for\n",
-    "# regions susieR flags as unreliable. ser_fallback and r_mismatch are orthogonal: ser_fallback = False\n",
-    "# only disables the SER fallback (EB LD-mismatch stays on); pass r_mismatch = 'none' too for the\n",
-    "# pre-change plain multi-effect fit.\n",
-    "parameter: ser_fallback = True    # fall back to single-effect (SER) when susieR flags R unreliable\n",
-    "parameter: r_finite = ''          # finite-sample R size; empty -> auto (LD-panel sample size)\n",
-    "parameter: r_mismatch = 'eb'      # LD-mismatch correction: 'eb' (default) or 'none'\n",
-    "parameter: r_mismatch_method = '' # rMismatch estimator 'mle'|'map'; empty -> pecotmr default\n",
-    "parameter: check_prior = ''       # susie_rss check_prior 'TRUE'|'FALSE'; empty -> pecotmr default\n",
-    "# --- plot opt-out ---------------------------------------------------\n",
-    "parameter: no_plot = False\n",
-    "# --- output prefix for the manifest file ----------------------------\n",
-    "parameter: manifest_name = 'gwas_rss'\n",
-    "# --- infrastructure -------------------------------------------------\n",
-    "parameter: container = ''\n",
-    "parameter: job_size = 1\n",
-    "parameter: walltime = '2h'\n",
-    "parameter: mem = '16G'\n",
-    "parameter: numThreads = 1"
-   ]
+   "source": "[global]\nparameter: cwd = path('output')\nparameter: modular_script_dir = path('code/script')\n# --- per-study GWAS inputs (use either or both) ---------------------\nparameter: gwas_meta = path('.')\nparameter: gwas_tsv_list = []   # list of STUDY=PATH items\n# --- region inputs (use either or both) -----------------------------\nparameter: region_list = path('.')\nparameter: regions = []         # list of chr:start-end strings\n# --- LD reference + genome ------------------------------------------\nparameter: ld_meta = path\nparameter: genome = 'GRCh38'\n# --- QC knobs (forwarded to gwas_sumstats_construct.R) --------------\nparameter: qc_method = 'none'   # none | slalom | dentist\nparameter: impute = False\nparameter: qc_args = ''         # JSON object spliced into summaryStatsQc()\nparameter: maf = 0.0025         # MAF cutoff (summaryStatsQc mafCutoff); 0 disables\nparameter: skip_regions = []    # chr:start-end window(s) whose variants are dropped (skipRegion)\nparameter: skip_analysis_pip_cutoff = 0.025   # skip a region below this max PIP (pipCutoffToSkip); 0 disables\nparameter: allele_flip_kriging = False   # kriging allele-flip QC: sign-flip switched z (logLR>2 & |z|>2); off by default\nparameter: effective_n = True   # case/control: use effective sample size 4/(1/n_case+1/n_control) as N (summaryStatsQc effectiveN); False -> raw N\n# --- fine-mapping knobs (forwarded to fine_mapping.R) ---------------\nparameter: methods = 'susie'\nparameter: coverage = 0.95\nparameter: secondary_coverage = '0.7,0.5'\nparameter: min_abs_corr = 0.8\nparameter: median_abs_corr = ''   # empty -> off (OR-logic purity; needs pecotmr step-1)\nparameter: pip_cutoff = 0.025\nparameter: L = 20\nparameter: L_greedy = 5\nparameter: method_args = ''     # nested per-method JSON object\n# GWAS SuSiE-RSS fine-mapping: SER fallback is ON by default (reproduces the single-panel notebook):\n# fit finite-sample R + EB LD-mismatch SuSiE-RSS and fall back to the single-effect (SER) result for\n# regions susieR flags as unreliable. ser_fallback and r_mismatch are orthogonal: ser_fallback = False\n# only disables the SER fallback (EB LD-mismatch stays on); pass r_mismatch = 'none' too for the\n# pre-change plain multi-effect fit. Requires susieR >= 0.16.6 (which moved R_mismatch_method /\n# check_prior into susie_rss_control(); pass those and other control settings via rss_control).\nparameter: ser_fallback = True    # fall back to single-effect (SER) when susieR flags R unreliable\nparameter: r_finite = ''          # finite-sample R size; empty -> auto (LD-panel sample size)\nparameter: r_mismatch = 'eb_mix'  # LD-mismatch correction: 'none' | 'eb' | 'eb_mix' (residual-mixture EB, default)\nparameter: rss_control = ''       # JSON object of susie_rss_control() settings, e.g. '{\"check_prior\":true,\"mismatch_estimator\":\"map\"}'; empty -> defaults\n# --- plot opt-out ---------------------------------------------------\nparameter: no_plot = False\n# --- output prefix for the manifest file ----------------------------\nparameter: manifest_name = 'gwas_rss'\n# --- infrastructure -------------------------------------------------\nparameter: container = ''\nparameter: job_size = 1\nparameter: walltime = '2h'\nparameter: mem = '16G'\nparameter: numThreads = 1"
   },
   {
    "cell_type": "code",
@@ -227,30 +175,7 @@
     "kernel": "SoS"
    },
    "outputs": [],
-   "source": [
-    "[gwas_fine_mapping]\n",
-    "# Per-RDS fan-out: one fine-mapping task per (study, region) GwasSumStats.\n",
-    "output: f\"{cwd}/fine_mapping/{_input:bnn}.gwas_finemap.rds\", group_by = 1\n",
-    "task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads, tags = f\"{step_name}_{_output:bn}\"\n",
-    "bash: expand = '${ }', stderr = f\"{_output}.stderr\", stdout = f\"{_output}.stdout\", container = container\n",
-    "    Rscript ${modular_script_dir}/pecotmr_integration/fine_mapping.R \\\n",
-    "        --gwas-sumstats ${_input} \\\n",
-    "        --methods ${methods} \\\n",
-    "        --coverage ${coverage} \\\n",
-    "        --secondary-coverage ${secondary_coverage} \\\n",
-    "        --min-abs-corr ${min_abs_corr} \\\n",
-    "        --pip-cutoff ${pip_cutoff} \\\n",
-    "        --L ${L} \\\n",
-    "        --L-greedy ${L_greedy} \\\n",
-    "        ${('--median-abs-corr ' + str(median_abs_corr)) if str(median_abs_corr) != '' else ''} \\\n",
-    "        ${('--method-args ' + repr(method_args)) if method_args else ''} \\\n",
-    "        --ser-fallback ${'TRUE' if ser_fallback else 'FALSE'} \\\n",
-    "        --r-mismatch ${r_mismatch} \\\n",
-    "        ${('--r-finite ' + str(r_finite)) if str(r_finite) != '' else ''} \\\n",
-    "        ${('--r-mismatch-method ' + r_mismatch_method) if r_mismatch_method else ''} \\\n",
-    "        ${('--check-prior ' + check_prior) if check_prior else ''} \\\n",
-    "        --output ${_output}"
-   ]
+   "source": "[gwas_fine_mapping]\n# Per-RDS fan-out: one fine-mapping task per (study, region) GwasSumStats.\noutput: f\"{cwd}/fine_mapping/{_input:bnn}.gwas_finemap.rds\", group_by = 1\ntask: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads, tags = f\"{step_name}_{_output:bn}\"\nbash: expand = '${ }', stderr = f\"{_output}.stderr\", stdout = f\"{_output}.stdout\", container = container\n    Rscript ${modular_script_dir}/pecotmr_integration/fine_mapping.R \\\n        --gwas-sumstats ${_input} \\\n        --methods ${methods} \\\n        --coverage ${coverage} \\\n        --secondary-coverage ${secondary_coverage} \\\n        --min-abs-corr ${min_abs_corr} \\\n        --pip-cutoff ${pip_cutoff} \\\n        --L ${L} \\\n        --L-greedy ${L_greedy} \\\n        ${('--median-abs-corr ' + str(median_abs_corr)) if str(median_abs_corr) != '' else ''} \\\n        ${('--method-args ' + repr(method_args)) if method_args else ''} \\\n        --ser-fallback ${'TRUE' if ser_fallback else 'FALSE'} \\\n        --r-mismatch ${r_mismatch} \\\n        ${('--r-finite ' + str(r_finite)) if str(r_finite) != '' else ''} \\\n        ${('--rss-control ' + repr(rss_control)) if rss_control else ''} \\\n        --output ${_output}"
   },
   {
    "cell_type": "code",
diff --git a/code/script/pecotmr_integration/fine_mapping.R b/code/script/pecotmr_integration/fine_mapping.R
index 3dbfd7c5..3299c466 100644
--- a/code/script/pecotmr_integration/fine_mapping.R
+++ b/code/script/pecotmr_integration/fine_mapping.R
@@ -119,8 +119,8 @@ parser <- add_argument(parser, "--pip-cutoff-to-skip",
 # fallback is ON by default (reproduces the single-panel notebook): fit a
 # finite-sample R + EB LD-mismatch SuSiE-RSS and drop to the single-effect (SER)
 # result for regions susieR flags as unreliable. These ride on gwas_args (GWAS
-# mode only); rFinite/rMismatchMethod/checkPrior forward only when set, so the
-# call also runs against a pecotmr that predates them.
+# mode only); rFinite forwards only when set. susie_rss_control() settings
+# (susieR >= 0.16.6) are passed as a JSON object via --rss-control.
 parser <- add_argument(parser, "--ser-fallback",
                        help = "GWAS mode: TRUE/FALSE. Fall back to the single-effect (SER) result when susieR flags R unreliable (fineMappingPipeline serFallback). Default TRUE.",
                        type = "character", default = "TRUE")
@@ -128,13 +128,10 @@ parser <- add_argument(parser, "--r-finite",
                        help = "GWAS mode: finite-sample R correction size (fineMappingPipeline rFinite). Empty = auto (LD-panel sample size).",
                        type = "character", default = "")
 parser <- add_argument(parser, "--r-mismatch",
-                       help = "GWAS mode: LD-mismatch correction (fineMappingPipeline rMismatch): 'eb' (default) or 'none'.",
-                       type = "character", default = "eb")
-parser <- add_argument(parser, "--r-mismatch-method",
-                       help = "GWAS mode: rMismatch estimator (fineMappingPipeline rMismatchMethod): 'mle' or 'map'. Empty = pecotmr default.",
-                       type = "character", default = "")
-parser <- add_argument(parser, "--check-prior",
-                       help = "GWAS mode: TRUE/FALSE for susie_rss check_prior (fineMappingPipeline checkPrior). Empty = pecotmr default.",
+                       help = "GWAS mode: LD-mismatch correction (fineMappingPipeline rMismatch): 'none', 'eb', or 'eb_mix' (residual-mixture EB, susieR >= 0.16.6). Default 'eb_mix'.",
+                       type = "character", default = "eb_mix")
+parser <- add_argument(parser, "--rss-control",
+                       help = "GWAS mode: JSON object of susieR::susie_rss_control() settings (e.g. '{\"check_prior\":true,\"mismatch_estimator\":\"map\"}'), forwarded as fineMappingPipeline rssControl. Empty = susie_rss_control() defaults.",
                        type = "character", default = "")
 # --- Multivariate / joint-fit knobs (QTL mode; mvsusie / fsusie). Each is
 # opt-in and omitted from the pipeline call when left at its default, so this
@@ -317,18 +314,23 @@ if (has_gwas) {
   ser_fallback <- as.logical(argv$ser_fallback)
   if (is.na(ser_fallback))
     stop("--ser-fallback must be TRUE or FALSE (got: ", argv$ser_fallback, ")")
-  # GWAS-only SuSiE-RSS knobs on top of the shared cs_args. rFinite /
-  # rMismatchMethod / checkPrior forward only when set (empty -> pecotmr default).
+  # GWAS-only SuSiE-RSS knobs on top of the shared cs_args. rFinite forwards
+  # only when set; --rss-control (JSON) becomes the rssControl named list of
+  # susie_rss_control() settings.
   gwas_args <- c(cs_args,
                  list(serFallback = ser_fallback,
                       rMismatch   = argv$r_mismatch))
   if (nzchar(argv$r_finite)) gwas_args$rFinite <- as.numeric(argv$r_finite)
-  if (nzchar(argv[["r_mismatch_method"]]))
-    gwas_args$rMismatchMethod <- argv[["r_mismatch_method"]]
-  if (nzchar(argv$check_prior)) {
-    cp <- as.logical(argv$check_prior)
-    if (is.na(cp)) stop("--check-prior must be TRUE or FALSE (got: ", argv$check_prior, ")")
-    gwas_args$checkPrior <- cp
+  if (nzchar(argv$rss_control) && argv$rss_control != "." &&
+      argv$rss_control != "{}") {
+    rc <- tryCatch(jsonlite::fromJSON(argv$rss_control, simplifyVector = TRUE),
+                   error = function(e) stop(
+                     "--rss-control must be a JSON object (got: ", argv$rss_control,
+                     "). Error: ", conditionMessage(e)))
+    if (!is.list(rc) || is.null(names(rc)) || any(!nzchar(names(rc))))
+      stop("--rss-control must be a JSON object with named fields, e.g. ",
+           '\'{"check_prior":true,"mismatch_estimator":"map"}\'.')
+    gwas_args$rssControl <- rc
   }
   res <- do.call(fineMappingPipeline, c(list(gss), gwas_args))
   label <- paste0("GwasSumStats '", basename(argv$gwas_sumstats), "'")