From d5b2dcd74198eec446cae58de1a6983a8c2f746b Mon Sep 17 00:00:00 2001
From: Peter van Heusden <pvanheusden@uwc.ac.za>
Date: Sat, 22 Feb 2025 08:45:35 +0200
Subject: [PATCH 1/4] Fix up tool_data_table_conf files

---
 tools/artic/artic_minion.xml                    |  2 +-
 tools/artic/tool-data/models.loc.sample         | 11 +----------
 tools/clair3/test-data/clair3_models.loc        | 13 ++++++-------
 tools/clair3/tool-data/clair3_models.loc.sample |  9 +++++++++
 tools/clair3/tool-data/model.loc.sample         | 11 -----------
 5 files changed, 17 insertions(+), 29 deletions(-)
 create mode 100644 tools/clair3/tool-data/clair3_models.loc.sample
 delete mode 100644 tools/clair3/tool-data/model.loc.sample

diff --git a/tools/artic/artic_minion.xml b/tools/artic/artic_minion.xml
index 8889c4ba386..4ec927204c6 100644
--- a/tools/artic/artic_minion.xml
+++ b/tools/artic/artic_minion.xml
@@ -1,4 +1,4 @@
-<tool id="artic_minion" name="ARTIC minion" version="@TOOL_VERSION@+galaxy0" profile="20.09">
+<tool id="artic_minion" name="ARTIC minion" version="@TOOL_VERSION@+galaxy1" profile="23.2">
     <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/artic/tool-data/models.loc.sample b/tools/artic/tool-data/models.loc.sample
index c71b09beae5..f07d88e2ccf 100644
--- a/tools/artic/tool-data/models.loc.sample
+++ b/tools/artic/tool-data/models.loc.sample
@@ -1,13 +1,4 @@
-#Enter the model names in the second column, the platform name in the second and the path in the third.
-#This file lists the locations and dbkeys of all the model files
-#under the "models" directory (a directory that contains a directory
-#for each build). This file has the format (white space characters are
-#TAB characters):
-#
-#<id>    <name>    <platform>    <path>
-#
-#So, all_model.loc could look something like this:
-test_model	"the_model_name"	r941_prom_hac_g360+g422	$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422#This file lists the names and locations of all the clair3 model files
+#This file lists the names and locations of all the clair3 model files
 #under the "clair3_models" directory (a directory that contains a directory
 #for each build). This file has the format (white space characters are
 #TAB characters):
diff --git a/tools/clair3/test-data/clair3_models.loc b/tools/clair3/test-data/clair3_models.loc
index 896c2831b4a..2a7a2820b78 100644
--- a/tools/clair3/test-data/clair3_models.loc
+++ b/tools/clair3/test-data/clair3_models.loc
@@ -1,11 +1,10 @@
-#Enter the model names in the second column, the platform name in the second and the path in the third.
-#This file lists the locations and dbkeys of all the model files
-#under the "models" directory (a directory that contains a directory
+#This file lists the names and locations of all the clair3 model files
+#under the "clair3_models" directory (a directory that contains a directory
 #for each build). This file has the format (white space characters are
 #TAB characters):
 #
-#<unique_build_id>  <display_name>   <platform> <file_path>	<source>
+#<unique_name>	<platform>	<sha256sum>	<file_path>	<source>
 #
-#So, all_model.loc could look something like this:
-test_model	"the_model_name"	ont	$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422	clair3
-r1041_e82_400bps_sup_v500	r1041_e82_400bps_sup_v500	ont	/no/such/model	rerio
+#So, clair3_models.loc could look something like this:
+test_model	ont		$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422	clair3
+r1041_e82_400bps_sup_v500	r1041_e82_400bps_sup_v500	ont	01c05768661bdd7de611e6bae1043c43b7523a54b223e029c683bfac0db7a678	/no/such/model	rerio
diff --git a/tools/clair3/tool-data/clair3_models.loc.sample b/tools/clair3/tool-data/clair3_models.loc.sample
new file mode 100644
index 00000000000..f07d88e2ccf
--- /dev/null
+++ b/tools/clair3/tool-data/clair3_models.loc.sample
@@ -0,0 +1,9 @@
+#This file lists the names and locations of all the clair3 model files
+#under the "clair3_models" directory (a directory that contains a directory
+#for each build). This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_name>	<platform>	<sha256sum>	<file_path>	<source>
+#
+#So, clair3_models.loc could look something like this:
+test_model	ont		$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422	clair3
diff --git a/tools/clair3/tool-data/model.loc.sample b/tools/clair3/tool-data/model.loc.sample
deleted file mode 100644
index 477d23765be..00000000000
--- a/tools/clair3/tool-data/model.loc.sample
+++ /dev/null
@@ -1,11 +0,0 @@
-#Enter the model names in the second column, the platform name in the second and the path in the third.
-#This file lists the locations and dbkeys of all the model files
-#under the "models" directory (a directory that contains a directory
-#for each build). This file has the format (white space characters are
-#TAB characters):
-#
-#<unique_build_id>  <display_name>   <platform> <file_path>	<source>
-#
-#So, all_model.loc could look something like this:
-#test_model	r941_prom_hac_g360+g422		ont	$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422	clair3
-#r1041_e82_400bps_sup_v500	r1041_e82_400bps_sup_v500	ont	$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422	rerio

From a26b512de2c57da26a58895cfd77380c5224b820 Mon Sep 17 00:00:00 2001
From: Peter van Heusden <pvanheusden@uwc.ac.za>
Date: Sat, 22 Feb 2025 08:46:34 +0200
Subject: [PATCH 2/4] Remember to save this time

---
 tools/clair3/clair3.xml                      | 2 +-
 tools/clair3/tool_data_table_conf.xml.sample | 4 ++--
 tools/clair3/tool_data_table_conf.xml.test   | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/clair3/clair3.xml b/tools/clair3/clair3.xml
index e9fafb97647..fb84c266ff5 100644
--- a/tools/clair3/clair3.xml
+++ b/tools/clair3/clair3.xml
@@ -2,7 +2,7 @@
     <description>germline small variant caller for long-reads</description>
     <macros>
         <token name="@TOOL_VERSION@">1.0.10</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <xrefs>
         <xref type='bio.tools'>clair3</xref>
diff --git a/tools/clair3/tool_data_table_conf.xml.sample b/tools/clair3/tool_data_table_conf.xml.sample
index 42f07308dd8..9309dd45f01 100644
--- a/tools/clair3/tool_data_table_conf.xml.sample
+++ b/tools/clair3/tool_data_table_conf.xml.sample
@@ -2,8 +2,8 @@
 <tables>
     <!-- Locations of clair3 model folders -->
     <table name="model" comment_char="#">
-        <columns>value, name, platform, path, source</columns>
-        <file path="tool-data/model.loc" />
+        <columns>value, platform, sha256, path, source</columns>
+        <file path="tool-data/clair3_models.loc" />
     </table>
     <table name="all_fasta" comment_char="#">
         <columns>value, dbkey, name, path</columns>
diff --git a/tools/clair3/tool_data_table_conf.xml.test b/tools/clair3/tool_data_table_conf.xml.test
index 41bef973044..9732707a1ef 100644
--- a/tools/clair3/tool_data_table_conf.xml.test
+++ b/tools/clair3/tool_data_table_conf.xml.test
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
 <tables>
-    <!-- Locations of model folders -->
+    <!-- Locations of clair3 model folders -->
     <table name="clair3_models" comment_char="#">
-        <columns>value, name, platform, path, source</columns>
+        <columns>value, platform, sha256, path, source</columns>
         <file path="${__HERE__}/test-data/clair3_models.loc" />
     </table>
     <!-- Locations of reference genome files in fasta format -->

From ef8d97b4f0b02ffea2c272daf83a2cf14270c1b8 Mon Sep 17 00:00:00 2001
From: Peter van Heusden <pvanheusden@uwc.ac.za>
Date: Sat, 22 Feb 2025 09:13:01 +0200
Subject: [PATCH 3/4] Fix columns in test-data

---
 tools/artic/test-data/clair3_models.loc  | 2 +-
 tools/clair3/test-data/clair3_models.loc | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/artic/test-data/clair3_models.loc b/tools/artic/test-data/clair3_models.loc
index 2a7a2820b78..d0a41c3a1f3 100644
--- a/tools/artic/test-data/clair3_models.loc
+++ b/tools/artic/test-data/clair3_models.loc
@@ -7,4 +7,4 @@
 #
 #So, clair3_models.loc could look something like this:
 test_model	ont		$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422	clair3
-r1041_e82_400bps_sup_v500	r1041_e82_400bps_sup_v500	ont	01c05768661bdd7de611e6bae1043c43b7523a54b223e029c683bfac0db7a678	/no/such/model	rerio
+r1041_e82_400bps_sup_v500	ont	01c05768661bdd7de611e6bae1043c43b7523a54b223e029c683bfac0db7a678	/no/such/model	rerio
diff --git a/tools/clair3/test-data/clair3_models.loc b/tools/clair3/test-data/clair3_models.loc
index 2a7a2820b78..d0a41c3a1f3 100644
--- a/tools/clair3/test-data/clair3_models.loc
+++ b/tools/clair3/test-data/clair3_models.loc
@@ -7,4 +7,4 @@
 #
 #So, clair3_models.loc could look something like this:
 test_model	ont		$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422	clair3
-r1041_e82_400bps_sup_v500	r1041_e82_400bps_sup_v500	ont	01c05768661bdd7de611e6bae1043c43b7523a54b223e029c683bfac0db7a678	/no/such/model	rerio
+r1041_e82_400bps_sup_v500	ont	01c05768661bdd7de611e6bae1043c43b7523a54b223e029c683bfac0db7a678	/no/such/model	rerio

From e44d3cd8efa7b9178145a3f7c39aab9cbaf0ad2c Mon Sep 17 00:00:00 2001
From: Peter van Heusden <pvanheusden@uwc.ac.za>
Date: Wed, 26 Feb 2025 16:47:03 +0200
Subject: [PATCH 4/4] Correct tool data table name

---
 tools/clair3/tool_data_table_conf.xml.sample | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/clair3/tool_data_table_conf.xml.sample b/tools/clair3/tool_data_table_conf.xml.sample
index 9309dd45f01..9f75181a4fc 100644
--- a/tools/clair3/tool_data_table_conf.xml.sample
+++ b/tools/clair3/tool_data_table_conf.xml.sample
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tables>
     <!-- Locations of clair3 model folders -->
-    <table name="model" comment_char="#">
+    <table name="clair3_models" comment_char="#">
         <columns>value, platform, sha256, path, source</columns>
         <file path="tool-data/clair3_models.loc" />
     </table>