Add -project-dir option to lint command

docs/reference/cli.md

@@ -915,14 +915,20 @@ The `lint` command parses and analyzes the given Nextflow scripts and config fil
 **Options**
 
 `-exclude`
-: File pattern to exclude from linting. Can be specified multiple times (default: `.git, .nf-test, work`).
+: File pattern to exclude from linting (default: `.git, .lineage, .nextflow, .nf-test, nf-test.config, work`).
+: Can be specified multiple times.
 
 `-format`
 : Format scripts and config files that have no errors.
 
 `-o, -output`
 : Output mode for reporting errors: `full`, `extended`, `concise`, `json`, `markdown` (default: `full`).
 
+`-project-dir`
+: :::{versionadded} 26.04.0
+  :::
+: Path to project directory (default: `'.'`). Used to locate project-level assets such as the lib directory and modules directory.
+
 `-sort-declarations`
 : Sort script declarations in Nextflow scripts (default: `false`).
 

modules/nextflow/src/main/groovy/nextflow/Session.groovy

@@ -80,7 +80,7 @@ import nextflow.trace.event.FilePublishEvent
 import nextflow.trace.event.TaskEvent
 import nextflow.trace.event.WorkflowOutputEvent
 import nextflow.util.Barrier
-import nextflow.util.ConfigHelper
+import nextflow.util.ClassLoaderFactory
 import nextflow.util.Duration
 import nextflow.util.HistoryFile
 import nextflow.util.LoggerHelper
@@ -602,21 +602,8 @@ class Session implements ISession {
     ScriptBinding getBinding() { binding }
 
     @Memoized
-    ClassLoader getClassLoader() { getClassLoader0() }
-
-    @PackageScope
-    ClassLoader getClassLoader0() {
-        // extend the class-loader if required
-        final gcl = new GroovyClassLoader()
-        final libraries = ConfigHelper.resolveClassPaths(getLibDir())
-
-        for( Path lib : libraries ) {
-            def path = lib.complete()
-            log.debug "Adding to the classpath library: ${path}"
-            gcl.addClasspath(path.toString())
-        }
-
-        return gcl
+    ClassLoader getClassLoader() {
+        ClassLoaderFactory.create(getLibDir())
     }
 
     Barrier getBarrier() { monitorsBarrier }

modules/nextflow/src/main/groovy/nextflow/cli/CmdLint.groovy

@@ -40,6 +40,7 @@ import nextflow.script.formatter.ScriptFormattingVisitor
 import nextflow.script.parser.v2.ErrorListener
 import nextflow.script.parser.v2.ErrorSummary
 import nextflow.script.parser.v2.StandardErrorListener
+import nextflow.util.ClassLoaderFactory
 import nextflow.util.PathUtils
 import org.codehaus.groovy.control.SourceUnit
 import org.codehaus.groovy.control.messages.SyntaxErrorMessage
@@ -62,7 +63,7 @@ class CmdLint extends CmdBase {
         names = ['-exclude'],
         description = 'File pattern to exclude from error checking (can be specified multiple times)'
     )
-    List<String> excludePatterns = ['.git', '.lineage', '.nf-test', '.nextflow', 'work', 'nf-test.config']
+    List<String> excludePatterns = ['.git', '.lineage', '.nextflow', '.nf-test', 'nf-test.config', 'work']
 
     @Parameter(
         names = ['-o', '-output'],
@@ -82,6 +83,12 @@ class CmdLint extends CmdBase {
         }
     }
 
+    @Parameter(
+        names = ['-project-dir'],
+        description = 'Path to project directory (default: .)'
+    )
+    String projectDir = '.'
+
     @Parameter(names = ['-format'], description = 'Format scripts and config files that have no errors')
     boolean formatting
 
@@ -121,7 +128,11 @@ class CmdLint extends CmdBase {
         if( !spaces && !tabs )
             spaces = 4
 
-        scriptParser = new ScriptParser()
+        final baseDir = Path.of(projectDir)
+        final libDir = baseDir.resolve('lib')
+        final classLoader = ClassLoaderFactory.create([ libDir ])
+
+        scriptParser = new ScriptParser(baseDir, classLoader)
         configParser = new ConfigParser()
         errorListener = outputMode == 'json'
             ? new JsonErrorListener()

modules/nextflow/src/main/groovy/nextflow/util/ClassLoaderFactory.groovy

@@ -0,0 +1,78 @@
+/*
+ * Copyright 2013-2025, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package nextflow.util
+
+import java.nio.file.Path
+
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+/**
+ * Helper methods to create class loaders with
+ * additional classpaths.
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@Slf4j
+@CompileStatic
+class ClassLoaderFactory {
+
+    /**
+     * Create a class loader with the given directories
+     * added to the classpath.
+     *
+     * @param dirs
+     */
+    static GroovyClassLoader create(List<Path> dirs) {
+        final gcl = new GroovyClassLoader()
+        final libraries = resolveClassPaths(dirs)
+        for( final lib : libraries ) {
+            gcl.addClasspath(lib.complete().toString())
+        }
+        return gcl
+    }
+
+    /**
+     * Given a list of directories, look for the files ending with
+     * the '.jar' extension and return a list containing the original
+     * directories and the JAR paths.
+     *
+     * @param dirs
+     */
+    static List<Path> resolveClassPaths(List<Path> dirs) {
+
+        List<Path> result = []
+
+        if( !dirs )
+            return result
+
+        for( final path : dirs ) {
+            if( path.isFile() && path.name.endsWith('.jar') ) {
+                result << path
+            }
+            else if( path.isDirectory() ) {
+                result << path
+                path.eachFileMatch( ~/.+\.jar$/ ) {
+                    if( it.isFile() )
+                        result << it
+                }
+            }
+        }
+
+        return result
+    }
+
+}

modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy

@@ -16,8 +16,6 @@
 
 package nextflow.util
 
-import java.nio.file.Path
-
 import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
@@ -69,32 +67,6 @@ class ConfigHelper {
         return obj
     }
 
-    /**
-     * Given a list of paths looks for the files ending with the extension '.jar' and return
-     * a list containing the original directories, plus the JARs paths
-     *
-     * @param dirs
-     * @return
-     */
-    static List<Path> resolveClassPaths( List<Path> dirs ) {
-
-        List<Path> result = []
-        if( !dirs )
-            return result
-
-        for( Path path : dirs ) {
-            if( path.isFile() && path.name.endsWith('.jar') ) {
-                result << path
-            }
-            else if( path.isDirectory() ) {
-                result << path
-                path.eachFileMatch( ~/.+\.jar$/ ) { if(it.isFile()) result << it }
-            }
-        }
-
-        return result
-    }
-
     static private final String TAB = '   '
 
     static private void canonicalFormat(StringBuilder writer, ConfigObject object, int level, boolean sort, List stack) {

modules/nextflow/src/main/groovy/nextflow/util/RemoteSession.groovy

@@ -54,7 +54,7 @@ class RemoteSession implements Serializable, Closeable {
     private transient List<Path> localPaths = deserialiseClasspath()
 
     @Lazy
-    private transient List<Path> resolvedClasspath = ConfigHelper.resolveClassPaths(localPaths)
+    private transient List<Path> resolvedClasspath = ClassLoaderFactory.resolveClassPaths(localPaths)
 
     protected RemoteSession() { }
 

modules/nextflow/src/test/groovy/nextflow/cli/CmdLintTest.groovy

@@ -81,4 +81,39 @@ class CmdLintTest extends Specification {
         dir?.deleteDir()
     }
 
+    def 'should add lib directory to class loader' () {
+
+        given:
+        def dir = Files.createTempDirectory('test')
+
+        dir.resolve('main.nf').text = '''\
+            println Utils.hello()
+            '''
+
+        dir.resolve('lib').mkdir()
+        dir.resolve('lib/Utils.groovy').text = '''\
+            class Utils {
+
+                String hello() {
+                    return 'Hello!'
+                }
+            }
+            '''
+
+        when:
+        def cmd = new CmdLint()
+        cmd.args = [dir.toString()]
+        cmd.projectDir = dir.toString()
+        cmd.launcher = Mock(Launcher) {
+            getOptions() >> Mock(CliOptions)
+        }
+        cmd.run()
+
+        then:
+        noExceptionThrown()
+
+        cleanup:
+        dir?.deleteDir()
+    }
+
 }

modules/nextflow/src/test/groovy/nextflow/util/ClassLoaderFactoryTest.groovy

@@ -0,0 +1,59 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package nextflow.util
+
+import java.nio.file.Files
+import java.nio.file.Path
+
+import spock.lang.Specification
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class ClassLoaderFactoryTest extends Specification {
+
+    def testResolveClasspaths() {
+
+        given:
+        def path1 = Files.createTempDirectory('path1')
+        path1.resolve('file1').text = 'File 1'
+        path1.resolve('file2.jar').text = 'File 2'
+        path1.resolve('dir').mkdir()
+        path1.resolve('dir/file3').text = 'File 3'
+        path1.resolve('dir/file4').text = 'File 4'
+
+        def path2 = Files.createTempDirectory('path2')
+        path2.resolve('file5').text = 'File 5'
+        path2.resolve('file6.jar').text = 'File 6'
+
+        def path3 = Path.of('/some/file')
+
+        when:
+        def list = ClassLoaderFactory.resolveClassPaths([path1, path2, path3])
+        then:
+        list.size() == 4
+        list.contains( path1 )
+        list.contains( path1.resolve('file2.jar') )
+        list.contains( path2 )
+        list.contains( path2.resolve('file6.jar') )
+
+        cleanup:
+        path1?.deleteDir()
+        path2?.deleteDir()
+    }
+
+}

modules/nextflow/src/test/groovy/nextflow/util/ConfigHelperTest.groovy

@@ -16,9 +16,6 @@
 
 package nextflow.util
 
-import java.nio.file.Files
-import java.nio.file.Paths
-
 import nextflow.config.ConfigClosurePlaceholder
 import spock.lang.Specification
 import spock.lang.Unroll
@@ -47,37 +44,6 @@ class ConfigHelperTest extends Specification {
 
     }
 
-    def testResolveClasspaths() {
-
-        given:
-        def path1 = Files.createTempDirectory('path1')
-        path1.resolve('file1').text = 'File 1'
-        path1.resolve('file2.jar').text = 'File 2'
-        path1.resolve('dir').mkdir()
-        path1.resolve('dir/file3').text = 'File 3'
-        path1.resolve('dir/file4').text = 'File 4'
-
-        def path2 = Files.createTempDirectory('path2')
-        path2.resolve('file5').text = 'File 5'
-        path2.resolve('file6.jar').text = 'File 6'
-
-        def path3 = Paths.get('/some/file')
-
-        when:
-        def list = ConfigHelper.resolveClassPaths([path1, path2, path3])
-        then:
-        list.size() == 4
-        list.contains( path1 )
-        list.contains( path1.resolve('file2.jar') )
-        list.contains( path2 )
-        list.contains( path2.resolve('file6.jar') )
-
-        cleanup:
-        path1?.deleteDir()
-        path2?.deleteDir()
-
-    }
-
     def 'should render config using properties notation' () {
 
         given: