Merge branch 'main' into features/name-as-tags

askimed · Jan 27, 2024 · a9049b0 · a9049b0
2 parents b954fa0 + 98c49e9
commit a9049b0
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Showing 3 changed files with 44 additions and 14 deletions.
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -4,22 +4,24 @@ on: [push, pull_request]
 
 jobs:
   test:
-
     runs-on: ubuntu-latest
-
+    strategy:
+      matrix:
+        java: [ '11', '17', '21' ]
+        nextflow: ['latest-edge', 'latest-stable' ]
     steps:
       - name: Checkout
         uses: actions/checkout@v2
 
-      - name: Install JDK 11
+      - name: Install JDK ${{ matrix.java }}
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: ${{ matrix.java }}
 
-      - name: Install Nextflow v22.10.4
-        run: |
-          export NXF_VER=22.10.4;curl -s https://get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - name: Setup Nextflow ${{ matrix.nextflow }}
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.nextflow }}"
 
       - name: Test
         run: mvn install
diff --git a/files/nf-test b/files/nf-test
@@ -15,6 +15,28 @@ update() {
   fi
 }
 
+# nf-test uses the same logic as Nextflow to ensure to pick up the same jvm.
+# https://github.com/nextflow-io/nextflow/blob/master/nextflow#L263
+if [[ "$NXF_JAVA_HOME" ]]; then
+  JAVA_HOME="$NXF_JAVA_HOME"
+  unset JAVA_CMD
+fi
+# Determine the Java command to use to start the JVM.
+if [ ! -x "$JAVA_CMD" ] ; then
+    if [ -d "$JAVA_HOME" ] ; then
+        if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+            # IBM's JDK on AIX uses strange locations for the executables
+            JAVA_CMD="$JAVA_HOME/jre/sh/java"
+        else
+            JAVA_CMD="$JAVA_HOME/bin/java"
+        fi
+    elif [ -x /usr/libexec/java_home ]; then
+        JAVA_CMD="$(/usr/libexec/java_home -v 1.8+)/bin/java"
+    else
+        JAVA_CMD="$(which java)" || JAVA_CMD=java
+    fi
+fi
+
 if test -f "${FOLDER}/${APP_JAR}"; then
   FILE_PATH_JAR=${FOLDER}/${APP_JAR}
 else

diff --git a/pom.xml b/pom.xml
@@ -24,8 +24,8 @@
 
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-		<java.version>1.8</java.version>
-		<maven.compiler.release>8</maven.compiler.release>
+		<java.version>11</java.version>
+		<maven.compiler.release>${java.version}</maven.compiler.release>
 		<maven.compiler.source>${java.version}</maven.compiler.source>
 		<maven.compiler.target>${java.version}</maven.compiler.target>
 		<junit.version>5.9.1</junit.version>
@@ -37,26 +37,26 @@
 		<dependency>
 			<groupId>org.codehaus.groovy</groupId>
 			<artifactId>groovy-all</artifactId>
-			<version>3.0.9</version>
+			<version>3.0.19</version>
 			<type>pom</type>
 		</dependency>
 
 		<dependency>
 			<groupId>org.codehaus.groovy</groupId>
 			<artifactId>groovy-nio</artifactId>
-			<version>3.0.9</version>
+			<version>3.0.19</version>
 		</dependency>
 
 		<dependency>
 			<groupId>org.codehaus.groovy</groupId>
 			<artifactId>groovy-yaml</artifactId>
-			<version>3.0.9</version>
+			<version>3.0.19</version>
 		</dependency>
 
 		<dependency>
 			<groupId>org.apache.ivy</groupId>
 			<artifactId>ivy</artifactId>
-			<version>2.5.0</version>
+			<version>2.5.2</version>
 		</dependency>
 
 		<dependency>
@@ -77,6 +77,12 @@
 			<version>4.4.2</version>
 		</dependency>
 
+		<dependency>
+			<groupId>org.yaml</groupId>
+			<artifactId>snakeyaml</artifactId>
+			<version>2.2</version>
+		</dependency>
+
 		<dependency>
 			<groupId>org.junit.jupiter</groupId>
 			<artifactId>junit-jupiter</artifactId>