From 1eeec1d8ae2adec32ba908c118364c2dbc6358c7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 30 Jul 2026 15:01:41 -0400
Subject: [PATCH 1/2] Fix ARTIC Clair3 data table declaration

---
 .../tool-data/{models.loc.sample => clair3_models.loc.sample} | 0
 tools/artic/tool_data_table_conf.xml.sample                   | 4 ++--
 tools/artic/tool_data_table_conf.xml.test                     | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)
 rename tools/artic/tool-data/{models.loc.sample => clair3_models.loc.sample} (100%)

diff --git a/tools/artic/tool-data/models.loc.sample b/tools/artic/tool-data/clair3_models.loc.sample
similarity index 100%
rename from tools/artic/tool-data/models.loc.sample
rename to tools/artic/tool-data/clair3_models.loc.sample
diff --git a/tools/artic/tool_data_table_conf.xml.sample b/tools/artic/tool_data_table_conf.xml.sample
index ca6f03d6794..47b2e3c0500 100644
--- a/tools/artic/tool_data_table_conf.xml.sample
+++ b/tools/artic/tool_data_table_conf.xml.sample
@@ -10,8 +10,8 @@
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/all_fasta.loc" />
     </table>
-    <table name="model" comment_char="#">
+    <table name="clair3_models" comment_char="#">
         <columns>value, platform, sha256, path, source</columns>
-        <file path="tool-data/model.loc" />
+        <file path="tool-data/clair3_models.loc" />
     </table>
 </tables>
diff --git a/tools/artic/tool_data_table_conf.xml.test b/tools/artic/tool_data_table_conf.xml.test
index 4412b6dd4e2..2943f93b3eb 100644
--- a/tools/artic/tool_data_table_conf.xml.test
+++ b/tools/artic/tool_data_table_conf.xml.test
@@ -9,7 +9,7 @@
         <columns>value, dbkey, name, path</columns>
         <file path="${__HERE__}/test-data/all_fasta.loc" />
     </table>
-    <table name="model" comment_char="#">
+    <table name="clair3_models" comment_char="#">
         <columns>value, platform, sha256, path, source</columns>
         <file path="${__HERE__}/test-data/clair3_models.loc" />
     </table>

From 9dc2ba14d580a17c788efa762c1e0aa370791d5d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 30 Jul 2026 15:57:49 -0400
Subject: [PATCH 2/2] Fix ARTIC MPXV protocol URL

---
 tools/artic/artic_minion.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/artic/artic_minion.xml b/tools/artic/artic_minion.xml
index 36210b55ecc..a36ce22bd58 100644
--- a/tools/artic/artic_minion.xml
+++ b/tools/artic/artic_minion.xml
@@ -416,7 +416,7 @@ For majority of users the default parameter values will result in a good consens
 - normalise: Increase this value to include more reads in the consensus generation step. This is per amplicon per strand, a value of a 100 would equate to an effective depth of 200. 
 - primer match threshold: When matching a read to a primer site, the pipeline allows for some deviation from the primer location. This value represents the max nucleotide distance between primer site and alignment position.
 
-.. _MPXV protocol: https://artic.network/mpxv/mpxv-bioinformatics-sop.html 
+.. _MPXV protocol: https://artic.network/fieldbioinformatics/fieldbioinformatics-sop.html
 .. _clair3: https://github.com/HKU-BAL/Clair3
 .. _Rerio: https://github.com/nanoporetech/rerio
 .. _can read here: https://raw.githubusercontent.com/nanoporetech/rerio/refs/heads/master/LICENCE.txt