Merge branch 'main' of https://github.com/quiltdata/nf-quilt

.github/workflows/mega-linter.yml

@@ -27,7 +27,7 @@ jobs:
     steps:
       # Git Checkout
       - name: Checkout Code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.PAT || secrets.GITHUB_TOKEN }}
           fetch-depth: 0 # If you use VALIDATE_ALL_CODEBASE = true, you can remove this line to improve performances
@@ -37,7 +37,7 @@ jobs:
         id: ml
         # You can override MegaLinter flavor used to have faster performances
         # More info at https://megalinter.github.io/flavors/
-        uses: oxsecurity/megalinter/flavors/dotnet@v7.8.0
+        uses: oxsecurity/megalinter/flavors/dotnet@v7.11.1
         env:
           # All available variables are described in documentation
           # https://megalinter.github.io/configuration/

.github/workflows/test.yml

@@ -27,7 +27,7 @@ jobs:
     steps:
     # Git Checkout
     - name: Checkout Code
-      uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
       with:
         token: ${{ secrets.GITHUB_TOKEN }}
         fetch-depth: 0
@@ -47,7 +47,7 @@ jobs:
         cache: gradle
 
     - name: Setup Gradle
-      uses: gradle/gradle-build-action@v2
+      uses: gradle/gradle-build-action@v3
 
     - name: Run Gradle Tests
       run: make test

build.gradle

@@ -98,7 +98,7 @@ allprojects {
         // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
         implementation 'com.github.groovy-wslite:groovy-wslite:1.1.3'
         implementation 'org.codehaus.groovy:groovy-all:3.0.21'
-        implementation 'com.fasterxml.jackson.core:jackson-databind:2.16.1'
+        implementation 'com.fasterxml.jackson.core:jackson-databind:2.17.1'
         implementation 'com.upplication:s3fs:2.2.2'
 
         modules {

plugins/nf-quilt/build.gradle

@@ -64,10 +64,10 @@ dependencies {
 
     // This dependency is exported to consumers, that is to say found on their compile classpath.
     compileOnly "io.nextflow:nextflow:$nextflowVersion"
-    compileOnly 'org.slf4j:slf4j-api:2.0.11'
+    compileOnly 'org.slf4j:slf4j-api:2.0.13'
     compileOnly 'org.pf4j:pf4j:3.11.0'
     // add here plugins depepencies
-    compileOnly 'org.slf4j:slf4j-simple:2.0.11'
+    compileOnly 'org.slf4j:slf4j-simple:2.0.13'
     compileOnly 'black.ninia:jep:4.2.0'
     runtime 'black.ninia:jep:4.2.0'
     runtimeOnly 'org.junit.platform:junit-platform-launcher:1.10.2'
@@ -81,7 +81,7 @@ dependencies {
     testImplementation "io.nextflow:nextflow:$nextflowVersion"
     testImplementation ("org.codehaus.groovy:groovy-test:3.0.21") { exclude group: 'org.codehaus.groovy' }
     testImplementation ("cglib:cglib-nodep:3.3.0")
-    testImplementation ("org.objenesis:objenesis:3.3")
+    testImplementation ("org.objenesis:objenesis:3.4")
     testImplementation ("org.spockframework:spock-core:2.3-groovy-3.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
     testImplementation ('org.spockframework:spock-junit4:2.3-groovy-3.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
     testImplementation ('com.google.jimfs:jimfs:1.3.0')