Merge branch 'main' into 244-support-dynamic-uris-or-metadata

.github/workflows/mega-linter.yml

@@ -27,7 +27,7 @@ jobs:
     steps:
       # Git Checkout
       - name: Checkout Code
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
         with:
           token: ${{ secrets.GITHUB_TOKEN }} # secrets.PAT || 
           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@v8.0.0
+        uses: oxsecurity/megalinter/flavors/dotnet@v8.1.0
         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@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
       with:
         token: ${{ secrets.GITHUB_TOKEN }}
         fetch-depth: 0

build.gradle

@@ -100,7 +100,7 @@ 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:3.0.22'
-        implementation 'com.fasterxml.jackson.core:jackson-databind:2.17.2'
+        implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.0'
         implementation 'com.upplication:s3fs:2.2.2'
 
         modules {

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.10.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.10.2-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

groovysh-task.gradle

@@ -21,7 +21,7 @@ gradle.projectsLoaded {
             }
 
             project.dependencies {
-                groovyshdependencies "org.apache.groovy:groovy-groovysh:4.0.22"
+                groovyshdependencies "org.apache.groovy:groovy-groovysh:4.0.23"
             }
 
             project.tasks.register('groovysh') {

plugins/nf-quilt/build.gradle

@@ -80,13 +80,13 @@ 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:2.1.0-alpha1'
-    compileOnly 'org.pf4j:pf4j:3.12.0'
+    compileOnly 'org.pf4j:pf4j:3.12.1'
     // add here plugins depepencies
     compileOnly 'org.slf4j:slf4j-simple:2.1.0-alpha1'
     compileOnly 'black.ninia:jep:4.2.0'
     runtime 'black.ninia:jep:4.2.0'
-    runtimeOnly 'org.junit.platform:junit-platform-launcher:1.11.0'
-    implementation 'commons-io:commons-io:2.16.1'
+    runtimeOnly 'org.junit.platform:junit-platform-launcher:1.11.2'
+    implementation 'commons-io:commons-io:2.17.0'
     implementation 'black.ninia:jep:4.2.0'
     testImplementation 'black.ninia:jep:4.2.0'
     //testImplementation(testFixtures('black.ninia:jep:4.0.3'))