From c783fdf6c62b8eb0d5d4d0d9a67e1b941b5f8488 Mon Sep 17 00:00:00 2001
From: Kiah McIntosh <kiah.mcintosh@nanoporetech.com>
Date: Fri, 8 May 2026 21:04:12 +0000
Subject: [PATCH] Increase prepareAnnotationReference memory [CW-7185]

---
 bin/workflow_glue/prepare_annotation_reference.py | 5 +++--
 subworkflows/transcriptome.nf                     | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/bin/workflow_glue/prepare_annotation_reference.py b/bin/workflow_glue/prepare_annotation_reference.py
index efab524..b047344 100644
--- a/bin/workflow_glue/prepare_annotation_reference.py
+++ b/bin/workflow_glue/prepare_annotation_reference.py
@@ -250,8 +250,9 @@ class Annotation:
                     if part
                 )
                 raise ValueError(
-                    "Failed to convert annotation to GTF with "
-                    "gffread:\n" + details
+                    "Failed to convert annotation to GTF with gffread.\n"
+                    f"Return code: {result.returncode}\n"
+                    "Error message:" + details
                 )
 
             if not dest.exists() or dest.stat().st_size < 1:
diff --git a/subworkflows/transcriptome.nf b/subworkflows/transcriptome.nf
index f473b4d..d8d8fed 100644
--- a/subworkflows/transcriptome.nf
+++ b/subworkflows/transcriptome.nf
@@ -6,7 +6,7 @@ OPTIONAL_FILE = file("$projectDir/data/OPTIONAL_FILE")
 process prepareAnnotationReference {
     label "wf_transcriptomes"
     cpus 1
-    memory "4 GB"
+    memory "6 GB"
     input:
         path ref_annotation
         path ref_genome