Improve build metadata generation and validation

- Move plugins-info.txt generation from buildInfo to releaseInfo task
- Add validation task to prevent releases with stale metadata
- Use GITHUB_RUN_NUMBER for build counter in CI to preserve incrementing across builds
- Validate build number and commit ID match GitHub Actions environment variables
- Add outputs.upToDateWhen { false } to ensure metadata tasks always run
- Update task documentation with detailed descriptions

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Signed-off-by: Paolo Di Tommaso <[email protected]>

Author: pditommaso

CLAUDE.md

@@ -124,7 +124,7 @@ Follow these actions to make a new release:
 - Run `make releaseInfo` to update the version number and generate checksums.
 - Run this command to stage for commit the release files:
     ```
-    git add VERSION changelog.txt nextflow nextflow.md5 nextflow.sha1 nextflow.sha256
+    git add VERSION changelog.txt nextflow nextflow.md5 nextflow.sha1 nextflow.sha256 modules/nextflow/src/main/resources/META-INF/plugins-info.txt
     ```
 - Make a commit using the `[release]` tag in the comment and push it upstream to trigger the release automation with GitHub action:
     ```

build.gradle

@@ -189,16 +189,26 @@ jar.enabled = false
 /*
  * Update the build timestamp in the source source file
  */
-task buildInfo { doLast {
+task buildInfo {
+    // Always run this task - never consider it up-to-date
+    outputs.upToDateWhen { false }
+
+    doLast {
 
     def file0 = file('modules/nextflow/src/main/resources/META-INF/build-info.properties')
     def buildNum = 0
-    def src = file0.text
-    src.find(/build *= *([0-9]*)/) { buildNum = it[1]?.toInteger()+1 }
-    if( !buildNum ) {
-        println "WARN: Unable to find current build number"
+
+    // Use GitHub Actions run number if available, otherwise increment local counter
+    if (System.getenv('GITHUB_RUN_NUMBER')) {
+        buildNum = System.getenv('GITHUB_RUN_NUMBER').toInteger()
+        println "Using GitHub Actions run number: $buildNum"
+    } else {
+        def src = file0.text
+        src.find(/build *= *([0-9]*)/) { buildNum = it[1]?.toInteger()+1 }
+        if( !buildNum ) {
+            println "WARN: Unable to find current build number"
+        }
     }
-    file0.text = src
 
     // -- update build-info file
     file0.text = """\
@@ -207,22 +217,24 @@ task buildInfo { doLast {
     timestamp=${System.currentTimeMillis()}
     commitId=${project.property('commitId')}
     """.stripIndent()
-
-
-    // -- create plugins-info file
-    def plugins = []
-    new File(rootProject.rootDir, 'plugins')
-            .eachDir { if(it.name.startsWith('nf-')) plugins << project(":plugins:${it.name}") }
-
-    def meta = plugins .collect { "$it.name@$it.version" }
-    file('modules/nextflow/src/main/resources/META-INF/plugins-info.txt').text = meta.toSorted().join('\n')
 }}
 
 /*
- * Update release information in nextflow wrapper and dockerfile
+ * Update release information in nextflow wrapper, dockerfile, and plugin metadata.
+ *
+ * This task:
+ * 1. Updates the NXF_VER version string in the nextflow launch script
+ * 2. Updates the release version in docker/Dockerfile
+ * 3. Generates plugins-info.txt with current plugin versions from VERSION files
+ *
+ * This task always runs to ensure all release artifacts are updated with current versions.
  */
-task releaseInfo { doLast {
-    
+task releaseInfo {
+    // Always run this task - never consider it up-to-date
+    outputs.upToDateWhen { false }
+
+    doLast {
+
     // -- update 'nextflow' wrapper
     def file0 = file('nextflow')
     def src = file0.text
@@ -234,8 +246,80 @@ task releaseInfo { doLast {
     src = file0.text
     src = src.replaceAll(/releases\/v[0-9a-zA-Z_\-\.]+\//, "releases/v$version/" as String)
     file0.text = src
+
+    // -- create plugins-info file
+    def plugins = []
+    new File(rootProject.rootDir, 'plugins')
+            .eachDir { if(it.name.startsWith('nf-')) plugins << project(":plugins:${it.name}") }
+    def meta = plugins.collect { "$it.name@$it.version" }
+    file('modules/nextflow/src/main/resources/META-INF/plugins-info.txt').text = meta.toSorted().join('\n')
 }}
 
+/*
+ * Validate that plugins-info.txt matches plugin VERSION files and that build-info.properties
+ * contains the correct build number and commit ID when running in GitHub Actions.
+ *
+ * This task ensures:
+ * 1. All plugin versions in plugins-info.txt match their corresponding VERSION files
+ * 2. The build number in build-info.properties matches GITHUB_RUN_NUMBER (in CI)
+ * 3. The commit ID in build-info.properties matches GITHUB_SHA (in CI)
+ *
+ * This validation prevents releases with stale or mismatched metadata.
+ */
+task validatePluginVersions {
+    dependsOn buildInfo
+    inputs.file('modules/nextflow/src/main/resources/META-INF/plugins-info.txt')
+    inputs.file('modules/nextflow/src/main/resources/META-INF/build-info.properties')
+    inputs.files(fileTree('plugins') { include '*/VERSION' })
+
+    doLast {
+        // Get expected versions from plugin projects
+        def expected = []
+        new File(rootProject.rootDir, 'plugins')
+            .eachDir { if(it.name.startsWith('nf-')) expected << project(":plugins:${it.name}") }
+        def expectedVersions = expected.collect { "$it.name@$it.version" }.toSorted()
+
+        // Get actual versions from plugins-info.txt
+        def actualVersions = file('modules/nextflow/src/main/resources/META-INF/plugins-info.txt').readLines()
+
+        // Compare plugin versions
+        if (expectedVersions != actualVersions) {
+            def diffs = []
+            expectedVersions.eachWithIndex { exp, i ->
+                def act = actualVersions.size() > i ? actualVersions[i] : 'missing'
+                if (exp != act) diffs << "  expected: $exp, actual: $act"
+            }
+            throw new GradleException("Plugin version mismatch:\n${diffs.join('\n')}\nRun 'make assemble' to fix.")
+        }
+
+        // Validate build-info.properties - require GitHub Actions environment variables
+        if (!System.getenv('GITHUB_RUN_NUMBER')) {
+            throw new GradleException("GITHUB_RUN_NUMBER environment variable is required")
+        }
+        if (!System.getenv('GITHUB_SHA')) {
+            throw new GradleException("GITHUB_SHA environment variable is required")
+        }
+
+        def buildInfoFile = file('modules/nextflow/src/main/resources/META-INF/build-info.properties')
+        def props = new Properties()
+        buildInfoFile.withInputStream { props.load(it) }
+
+        def actualBuild = props.getProperty('build')
+        def expectedBuild = System.getenv('GITHUB_RUN_NUMBER')
+        if (actualBuild != expectedBuild) {
+            throw new GradleException("Build number mismatch: build-info.properties has '${actualBuild}' but GITHUB_RUN_NUMBER is '${expectedBuild}'. Run 'make assemble' to fix.")
+        }
+
+        def actualCommit = props.getProperty('commitId')
+        def expectedCommit = System.getenv('GITHUB_SHA').take(9) // GitHub SHA is full hash, we use short form
+        if (actualCommit != expectedCommit) {
+            throw new GradleException("Commit ID mismatch: build-info.properties has '${actualCommit}' but GITHUB_SHA is '${expectedCommit}'. Run 'make assemble' to fix.")
+        }
+
+        println "✅ Build info validation passed: build=${actualBuild}, commitId=${actualCommit}"
+        println "✅ Plugin version validation passed: all ${expected.size()} plugin versions match"
+    }
+}
 
 /*
  * Compile sources and copies all libs to target directory
@@ -425,6 +509,7 @@ releaseInfo.finalizedBy makeDigest
 task upload {
     dependsOn compile
     dependsOn coreProjects.publish
+    dependsOn validatePluginVersions
 }
 
 

packing.gradle

@@ -126,7 +126,7 @@ task pack( dependsOn: [packOne, packDist]) {
 
 }
 
-task deploy( type: Exec, dependsOn: [clean, compile, pack]) {
+task deploy( type: Exec, dependsOn: [clean, compile, pack, validatePluginVersions]) {
 
     def temp = File.createTempFile('upload',null)
     temp.deleteOnExit()
@@ -233,10 +233,10 @@ task dockerPack(type: Exec, dependsOn: ['packOne']) {
 
 /*
  * Tag and upload the release
- * 
+ *
  * https://github.com/aktau/github-release/
  */
-task release(type: Exec, dependsOn: [pack, dockerImage]) {
+task release(type: Exec, dependsOn: [pack, dockerImage, validatePluginVersions]) {
 
     def launcherFile = file('nextflow').absoluteFile
     def launcherSha1 = file('nextflow.sha1').absoluteFile