From 051e60792c12589615e4accba0e7c86eb36fae84 Mon Sep 17 00:00:00 2001
From: Sam Nicholls <sam.nicholls@nanoporetech.com>
Date: Tue, 19 May 2026 09:29:48 +0100
Subject: [PATCH] Set conv.em to 1e-4 as documented

---
 bin/workflow_glue_r/R/bambu.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/bin/workflow_glue_r/R/bambu.R b/bin/workflow_glue_r/R/bambu.R
index a4666c3..5af7b5d 100644
--- a/bin/workflow_glue_r/R/bambu.R
+++ b/bin/workflow_glue_r/R/bambu.R
@@ -277,7 +277,10 @@ bambu_build_args <- function(args, reads, annotation_obj, discovery, quant) {
     if (quant) {
         # Chunked quant re-estimates degradation bias per chunk, which changes
         # the EM inputs and breaks equivalence with unchunked bambu quant.
-        bambu_args$opt.em <- list(degradationBias = FALSE)
+        # Use bambu's documented EM convergence threshold here. The looser
+        # implemented default (1e-2) leaves small deterministic chunk-vs-global
+        # quant discrepancies in the split workflow.
+        bambu_args$opt.em <- list(degradationBias = FALSE, conv = 1e-4)
     }
 
     bambu_args