Bump nextflow-parsing to Java 21 and align versions with dockstore

- Java 11 -> 21 (pom and template.yaml runtime java21)
- Groovy 3.0.8 -> 3.0.25 (3.0.8 cannot read Java 21 class files)
- fmt-maven-plugin -> com.spotify.fmt 2.29, dependency plugin 3.6.1,
  spotbugs 4.8.3.1, surefire/failsafe 3.5.3, compiler plugin 3.12.1
- jackson 2.22.1, guava 33.6.0-jre, slf4j-api 2.0.18, junit 5.9.1
- Ignore EI_EXPOSE_REP findings on NextflowHandler

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>

Author: denis-yuen

nextflow-parsing/NextflowParsingFunction/ignore.xml

@@ -13,4 +13,9 @@
     <Match>
         <Source name="ApiClient.java"/>
     </Match>
+    <!-- NextflowHandler is a simple bean; newer SpotBugs flags its getters/setters -->
+    <Match>
+        <Class name="io.dockstore.nextflowparsing.NextflowHandler"/>
+        <Bug pattern="EI_EXPOSE_REP,EI_EXPOSE_REP2"/>
+    </Match>
 </FindBugsFilter>

nextflow-parsing/NextflowParsingFunction/pom.xml

@@ -8,12 +8,12 @@
   <packaging>jar</packaging>
   <name>Nextflow parser created for SAM CLI.</name>
   <properties>
-    <maven-plugin-version>3.0.0-M5</maven-plugin-version>
-    <maven.compiler.source>11</maven.compiler.source>
-    <maven.compiler.target>11</maven.compiler.target>
-    <junit-version>5.7.2</junit-version>
+    <maven-plugin-version>3.5.3</maven-plugin-version>
+    <maven.compiler.source>21</maven.compiler.source>
+    <maven.compiler.target>21</maven.compiler.target>
+    <junit-version>5.9.1</junit-version>
     <jersey-version>2.34</jersey-version>
-    <jackson-version>2.22.0</jackson-version>
+    <jackson-version>2.22.1</jackson-version>
   </properties>
   <repositories>
     <repository>
@@ -83,17 +83,17 @@
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>slf4j-api</artifactId>
-      <version>1.7.31</version>
+      <version>2.0.18</version>
     </dependency>
     <dependency>
       <groupId>com.google.guava</groupId>
       <artifactId>guava</artifactId>
-      <version>32.0.0-jre</version>
+      <version>33.6.0-jre</version>
     </dependency>
     <dependency>
       <groupId>org.codehaus.groovy</groupId>
       <artifactId>groovy</artifactId>
-      <version>3.0.8</version>
+      <version>3.0.25</version>
     </dependency>
     <dependency>
       <groupId>io.dockstore</groupId>
@@ -135,7 +135,7 @@
           </execution>
         </executions>
         <groupId>org.apache.maven.plugins</groupId>
-        <version>3.2.0</version>
+        <version>3.6.1</version>
       </plugin>
       <plugin>
         <artifactId>spotbugs-maven-plugin</artifactId>
@@ -150,7 +150,7 @@
           </execution>
         </executions>
         <groupId>com.github.spotbugs</groupId>
-        <version>4.0.4</version>
+        <version>4.8.3.1</version>
       </plugin>
       <plugin>
         <artifactId>maven-checkstyle-plugin</artifactId>
@@ -189,8 +189,8 @@
             </goals>
           </execution>
         </executions>
-        <groupId>com.coveo</groupId>
-        <version>2.10</version>
+        <groupId>com.spotify.fmt</groupId>
+        <version>2.29</version>
       </plugin>
       <plugin>
         <artifactId>maven-shade-plugin</artifactId>
@@ -210,10 +210,10 @@
       <plugin>
         <artifactId>maven-compiler-plugin</artifactId>
         <groupId>org.apache.maven.plugins</groupId>
-        <version>3.8.1</version>
+        <version>3.12.1</version>
         <configuration>
-          <source>11</source>
-          <target>11</target>
+          <source>21</source>
+          <target>21</target>
         </configuration>
       </plugin>
     </plugins>

nextflow-parsing/template.yaml

@@ -16,7 +16,7 @@ Resources:
     Properties:
       CodeUri: NextflowParsingFunction
       Handler: helloworld.App::handleRequest
-      Runtime: java11
+      Runtime: java21
       MemorySize: 512
       Environment: # More info about Env Vars: https://github.com/awslabs/serverless-application-model/blob/master/versions/2016-10-31.md#environment-object
         Variables: