Update learnmsa for testng

Author: luisas

.nf-test.log

@@ -9,3 +9,36 @@ Nov-11 11:11:48.966 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand -
 Nov-11 11:11:48.968 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Started test plan
 Nov-11 11:11:48.968 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test pipeline' from file '/home/luisasantus/Desktop/multiplesequencealign/tests/default.nf.test'.
 Nov-11 11:11:48.968 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Run test '3b90429f: -profile test'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
+Nov-11 11:13:38.210 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '3b90429f: -profile test' finished. status: FAILED
+org.codehaus.groovy.runtime.powerassert.PowerAssertionError: assert workflow.success
+       |        |
+       workflow false
+	at org.codehaus.groovy.runtime.InvokerHelper.assertFailed(InvokerHelper.java:432)
+	at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.assertFailed(ScriptBytecodeAdapter.java:670)
+	at default_nf$_run_closure1$_closure2$_closure4.doCall(default.nf.test:25)
+	at default_nf$_run_closure1$_closure2$_closure4.doCall(default.nf.test)
+	at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
+	at java.base/java.lang.reflect.Method.invoke(Method.java:580)
+	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
+	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
+	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
+	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
+	at groovy.lang.Closure.call(Closure.java:427)
+	at groovy.lang.Closure.call(Closure.java:406)
+	at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16)
+	at com.askimed.nf.test.lang.pipeline.PipelineTest.execute(PipelineTest.java:135)
+	at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:172)
+	at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:322)
+	at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43)
+	at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18)
+	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
+	at picocli.CommandLine.access$1300(CommandLine.java:145)
+	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
+	at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
+	at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
+	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
+	at picocli.CommandLine.execute(CommandLine.java:2078)
+	at com.askimed.nf.test.App.run(App.java:39)
+	at com.askimed.nf.test.App.main(App.java:46)
+Nov-11 11:13:38.219 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test pipeline' finished. snapshot file: false, skipped tests: false, failed tests: true
+Nov-11 11:13:38.220 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 1 tests failed. Done!

assets/toolsheet.csv

@@ -1,3 +1,3 @@
 tree,args_tree,aligner,args_aligner
-FAMSA,,FAMSA,
-,,MAFFT,--dpparttree
+,,FAMSA,
+,,LEARNMSA,"--use_language_model"