Fix align-protein-sequences task to produce the score_ascii file

Author: hlfernandez

.vscode/tasks.json

@@ -0,0 +1,17 @@
+{
+    "version": "2.0.0",
+    "tasks": [
+        {
+            "label": "build",
+            "type": "shell",
+            "command": "compi-dk build -drd -tv",
+            "problemMatcher": []
+        },
+        {
+            "label": "publish [CompiHub]",
+            "type": "shell",
+            "command": "compi-dk hub-push --visible",
+            "problemMatcher": []
+        }
+    ]
+}

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [1.2.4] - 2023-06-22
+
+### Fixed
+
+- Add `score_ascii` to `-output` in `t_coffee` invocation of task `align-protein-sequences`.
+
 ## [1.2.3] - 2022-08-02
 
 ### Fixed

DATASETS.md

@@ -8,6 +8,7 @@ Download, uncompress it and move to the `ipssa-m-leprae` directory, where you wi
 
 ## Compatible versions
 
+- 1.2.4
 - 1.2.3
 - 1.2.2
 - 1.2.1

pipeline.xml

@@ -2,7 +2,7 @@
 
 <pipeline xmlns="http://www.sing-group.org/compi/pipeline-1.0"
 	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-	<version>1.2.3</version>
+	<version>1.2.4</version>
 
 	<params>
 		<param name="host_working_dir" shortName="hw" global="true">Path of the working directory in the host.</param>
@@ -142,7 +142,7 @@
 					;;
 			esac
 
-			docker run --rm -v ${host_working_dir}:/data pegi3s/tcoffee:${version_tcoffee} t_coffee /data/input/5_translated/${FILENAME} -method=${lowercase_align_method} -output=aln,fasta_aln,html -run_name /data/input/6_aligned/${FILENAME}
+			docker run --rm -v ${host_working_dir}:/data pegi3s/tcoffee:${version_tcoffee} t_coffee /data/input/5_translated/${FILENAME} -method=${lowercase_align_method} -output=aln,fasta_aln,html,score_ascii -run_name /data/input/6_aligned/${FILENAME}
 		</foreach>
 
 		<foreach id="back-translation" after="*align-protein-sequences" of="command" in="ls ${working_dir}/input/2_modified/*" as="file">