Fix remote modules when base dir is not the current working dir (#6932)

jorgee · pditommaso · bentsherman · web-flow · commit ca1e625ca45e · 2026-03-17T17:30:06.000-05:00
Co-authored-by: Paolo Di Tommaso &lt;paolo.ditommaso@gmail.com&gt;
Co-authored-by: Ben Sherman &lt;bentshermann@gmail.com&gt;
diff --git a/modules/nextflow/src/main/groovy/nextflow/exception/IllegalModulePathException.groovy b/modules/nextflow/src/main/groovy/nextflow/exception/IllegalModulePathException.groovy
@@ -24,5 +24,5 @@ import groovy.transform.InheritConstructors
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @InheritConstructors
-class IllegalModulePath extends Exception {
+class IllegalModulePathException extends Exception {
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/module/DefaultRemoteModuleResolver.groovy b/modules/nextflow/src/main/groovy/nextflow/module/DefaultRemoteModuleResolver.groovy
@@ -22,7 +22,7 @@ import nextflow.Global
 import nextflow.config.ConfigBuilder
 
 import nextflow.config.RegistryConfig
-import nextflow.exception.IllegalModulePath
+import nextflow.exception.IllegalModulePathException
 import nextflow.module.spi.RemoteModuleResolver
 
 import java.nio.file.Path
@@ -45,8 +45,8 @@ import java.nio.file.Path
 class DefaultRemoteModuleResolver implements RemoteModuleResolver {
 
     @Override
-    Path resolve(String moduleName, Path baseDir) {
-
+    Path resolve(String moduleName, Path projectDir) {
+        final baseDir = projectDir ?: Path.of('.').toAbsolutePath()
         final config = Global.config ?: new ConfigBuilder().setBaseDir(baseDir).build()
         final registryConfig = config.navigate('registry') as RegistryConfig
 
@@ -65,7 +65,7 @@ class DefaultRemoteModuleResolver implements RemoteModuleResolver {
             log.debug "Module ${reference} resolved to ${mainFile}"
             return mainFile
         } catch (Exception e) {
-            throw new IllegalModulePath("Failed to resolve remote module ${moduleName}: ${e.message}", e)
+            throw new IllegalModulePathException("Failed to resolve remote module ${moduleName}: ${e.message}", e)
         }
     }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/module/ModuleResolver.groovy b/modules/nextflow/src/main/groovy/nextflow/module/ModuleResolver.groovy
@@ -161,7 +161,7 @@ class ModuleResolver {
             // Install to modules directory (will compute directory checksum for future integrity checks)
             InstalledModule installed = storage.installModule(reference, version, tempFile, downloadUrl)
 
-            log.info "Module ${reference}@${version} installed successfully at ${installed.mainFile.parent}"
+            log.info "Module ${reference}@${version} installed successfully at ${installed.mainFile.parent.toAbsolutePath()}"
             return installed.mainFile
         }
         finally {
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy b/modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy
@@ -27,7 +27,7 @@ import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.NF
 import nextflow.Session
-import nextflow.exception.IllegalModulePath
+import nextflow.exception.IllegalModulePathException
 import nextflow.exception.ScriptCompilationException
 import nextflow.module.ModuleReference
 import nextflow.module.spi.RemoteModuleResolverProvider
@@ -167,7 +167,7 @@ class IncludeDef {
         final result = include as Path
         if( result.isAbsolute() ) {
             if( result.scheme == 'file' ) return result
-            throw new IllegalModulePath("Cannot resolve module path: ${result.toUriString()}")
+            throw new IllegalModulePathException("Cannot resolve module path: ${result.toUriString()}")
         }
         final str = include.toString()
         if( str.startsWith('./') || str.startsWith('../') ) {
@@ -212,10 +212,10 @@ class IncludeDef {
     @PackageScope
     void checkValidPath(path) {
         if( !path )
-            throw new IllegalModulePath("Missing module path attribute")
+            throw new IllegalModulePathException("Missing module path attribute")
 
         if( path instanceof Path && path.scheme != 'file' )
-            throw new IllegalModulePath("Remote modules are not allowed -- Offending module: ${path.toUriString()}")
+            throw new IllegalModulePathException("Remote modules are not allowed -- Offending module: ${path.toUriString()}")
 
         final str = path.toString()
         if( str.startsWith('/') || str.startsWith('./') || str.startsWith('../') || str.startsWith('plugin/') )
@@ -225,7 +225,7 @@ class IncludeDef {
         try {
             ModuleReference.parse(str)
         } catch( Exception e ) {
-            throw new IllegalModulePath("Module path must start with '/', './', '../' or 'plugin/' prefix, or be a valid remote module reference (scope/name) -- Offending module: $str")
+            throw new IllegalModulePathException("Module path must start with '/', './', '../' or 'plugin/' prefix, or be a valid remote module reference (scope/name) -- Offending module: $str")
         }
     }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/parser/v2/ScriptCompiler.java b/modules/nextflow/src/main/groovy/nextflow/script/parser/v2/ScriptCompiler.java
@@ -88,16 +88,18 @@ public class ScriptCompiler {
 
     private final CompilerConfiguration config;
     private final GroovyClassLoader loader;
+    private final Path projectDir;
 
     private Compiler compiler;
 
-    public ScriptCompiler(boolean debug, Path targetDirectory, ClassLoader parent) {
-        this(getConfig(debug, targetDirectory), parent);
+    public ScriptCompiler(boolean debug, Path targetDirectory, ClassLoader parent, Path projectDir) {
+        this(getConfig(debug, targetDirectory), parent, projectDir);
     }
 
-    public ScriptCompiler(CompilerConfiguration config, ClassLoader parent) {
+    public ScriptCompiler(CompilerConfiguration config, ClassLoader parent, Path projectDir) {
         this.config = config;
         this.loader = new GroovyClassLoader(parent, config);
+        this.projectDir = projectDir;
     }
 
     private static CompilerConfiguration getConfig(boolean debug, Path targetDirectory) {
@@ -269,7 +271,7 @@ public void addPhaseOperation(IPrimaryClassNodeOperation op, int phase) {
         private void analyze(SourceUnit source) {
             // on first pass, recursively add included modules to queue
             if( entry == null ) {
-                modules = new ModuleResolver(compiler).resolve(source, uri -> createSourceUnit(uri));
+                modules = new ModuleResolver(projectDir, compiler).resolve(source, uri -> createSourceUnit(uri));
                 for( var su : modules )
                     addSource(su);
                 entry = source;
@@ -283,7 +285,7 @@ private void analyze(SourceUnit source) {
             var cn = source.getAST().getClasses().get(0);
 
             // perform strict syntax checking
-            var includeResolver = new ResolveIncludeVisitor(source, compiler);
+            var includeResolver = new ResolveIncludeVisitor(source, projectDir, compiler);
             includeResolver.visit();
             for( var error : includeResolver.getErrors() )
                 source.getErrorCollector().addErrorAndContinue(error);
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/parser/v2/ScriptLoaderV2.groovy b/modules/nextflow/src/main/groovy/nextflow/script/parser/v2/ScriptLoaderV2.groovy
@@ -175,7 +175,7 @@ class ScriptLoaderV2 implements ScriptLoader {
 
     private ScriptCompiler getCompiler() {
         if( !compiler )
-            compiler = new ScriptCompiler(session.debug, session.classesDir, session.getClassLoader())
+            compiler = new ScriptCompiler(session.debug, session.classesDir, session.getClassLoader(), session.baseDir)
         return compiler
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/IncludeDefTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/IncludeDefTest.groovy
@@ -24,7 +24,7 @@ import java.nio.file.NoSuchFileException
 import java.nio.file.Path
 
 import nextflow.ast.NextflowDSL
-import nextflow.exception.IllegalModulePath
+import nextflow.exception.IllegalModulePathException
 import nextflow.file.FileHelper
 import org.codehaus.groovy.control.CompilerConfiguration
 import org.codehaus.groovy.control.customizers.ASTTransformationCustomizer
@@ -51,7 +51,7 @@ class IncludeDefTest extends Specification {
         when:
         include.resolveModulePath('http://foo.com/bar')
         then:
-        thrown(IllegalModulePath)
+        thrown(IllegalModulePathException)
 
     }
 
@@ -147,17 +147,17 @@ class IncludeDefTest extends Specification {
         when:
         include.checkValidPath('invalid!')
         then:
-        thrown(IllegalModulePath)
+        thrown(IllegalModulePathException)
 
         when:
         include.checkValidPath( 'http://foo.com/x.y')
         then:
-        thrown(IllegalModulePath)
+        thrown(IllegalModulePathException)
 
         when:
         include.checkValidPath(FileHelper.asPath('http://foo.com/x/y/z'))
         then:
-        thrown(IllegalModulePath)
+        thrown(IllegalModulePathException)
 
     }
 
diff --git a/modules/nf-lang/src/main/java/nextflow/module/spi/FallbackRemoteModuleResolver.java b/modules/nf-lang/src/main/java/nextflow/module/spi/FallbackRemoteModuleResolver.java
@@ -31,14 +31,15 @@
 public class FallbackRemoteModuleResolver implements RemoteModuleResolver {
 
     @Override
-    public Path resolve(String moduleName, Path baseDir) {
-        final var resolved = baseDir.resolve(moduleName).normalize();
-        // Prevent path traversal outside the base directory
-        if (!resolved.startsWith(baseDir.normalize())) {
-            throw new IllegalStateException("Invalid module name '" + moduleName + "' - path escapes the modules directory");
+    public Path resolve(String moduleName, Path projectDir) {
+        var baseDir = projectDir != null ? projectDir : Path.of(".").toAbsolutePath();
+        var modulesDir = baseDir.resolve("modules").normalize();
+        var resolved = modulesDir.resolve(moduleName).normalize();
+        if( !resolved.startsWith(modulesDir) ) {
+            throw new IllegalStateException("Invalid module name '" + moduleName + "' -- path escapes the modules directory");
         }
-        if (!Files.exists(resolved)) {
-            throw new IllegalStateException("Module '" + moduleName + "' not locally found at 'modules' folder - use 'nextflow module install' to download module files");
+        if( !Files.exists(resolved) ) {
+            throw new IllegalStateException("Module '" + moduleName + "' not found in 'modules' directory -- use 'nextflow module install' to install module first");
         }
         return resolved.resolve("main.nf");
     }
@@ -47,4 +48,4 @@ public Path resolve(String moduleName, Path baseDir) {
     public int getPriority() {
         return Integer.MIN_VALUE;  // Fallback has lowest possible priority
     }
-}
+}
diff --git a/modules/nf-lang/src/main/java/nextflow/module/spi/RemoteModuleResolver.java b/modules/nf-lang/src/main/java/nextflow/module/spi/RemoteModuleResolver.java
@@ -47,11 +47,11 @@ public interface RemoteModuleResolver {
      * </ol>
      *
      * @param moduleName The module reference string (e.g., '@scope/name' or '@scope/name@version')
-     * @param baseDir The base directory for the project (used to locate the modules directory)
+     * @param projectDir The base directory for the project (used to locate the modules directory)
      * @return Path to the resolved module's main.nf file
      * @throws IllegalArgumentException if the module reference is invalid or resolution fails
      */
-    Path resolve(String moduleName, Path baseDir);
+    Path resolve(String moduleName, Path projectDir);
 
     /**
      * Get the priority of this resolver. Higher priority resolvers are tried first.
@@ -65,4 +65,4 @@ public interface RemoteModuleResolver {
     default int getPriority() {
         return 0;
     }
-}
+}
diff --git a/modules/nf-lang/src/main/java/nextflow/script/control/ModuleResolver.java b/modules/nf-lang/src/main/java/nextflow/script/control/ModuleResolver.java
@@ -37,9 +37,11 @@
 public class ModuleResolver {
 
     private Compiler compiler;
+    private Path projectDir;
 
-    public ModuleResolver(Compiler compiler) {
+    public ModuleResolver(Path projectDir, Compiler compiler) {
         this.compiler = compiler;
+        this.projectDir = projectDir;
     }
 
     /**
@@ -74,17 +76,8 @@ private SourceUnit resolveInclude(IncludeNode node, SourceUnit sourceUnit, Funct
         if( source.startsWith("plugin/") )
             return null;
 
-        var parent = Path.of(sourceUnit.getSource().getURI()).getParent();
-
-        // Resolve remote module paths (scope/name format, not starting with local prefixes)
-        if( isRemoteModule(source) ) {
-            var modules = Path.of("./modules");
-            var resolver = RemoteModuleResolverProvider.getInstance();
-            resolver.resolve(source, modules.getParent());
-            parent = modules;
-        }
-
-        var includeUri = getIncludeUri(parent, source);
+        var uri = sourceUnit.getSource().getURI();
+        var includeUri = getIncludeUri(uri, source);
         if( compiler.getSource(includeUri) != null )
             return null;
         if( !Files.exists(Path.of(includeUri)) )
@@ -97,20 +90,33 @@ private SourceUnit resolveInclude(IncludeNode node, SourceUnit sourceUnit, Funct
         return includeSource;
     }
 
+    private URI getIncludeUri(URI uri, String source) {
+        if( isRemoteModule(source) ) {
+            return RemoteModuleResolverProvider.getInstance()
+                .resolve(source, projectDir)
+                .normalize()
+                .toUri();
+        }
+        else {
+            var parent = Path.of(uri).getParent();
+            return getLocalIncludeUri(parent, source);
+        }
+    }
+
     /**
      * Module name pattern matching the canonical format used by ModuleReference.
      * Scope: lowercase alphanumeric with dots/underscores/hyphens.
      * Name: one or more slash-separated segments, each lowercase alphanumeric with dots/underscores/hyphens.
      */
-    static final String REMOTE_MODULE_PATTERN = "^[a-z0-9][a-z0-9._\\-]*/[a-z][a-z0-9._\\-]*(/[a-z][a-z0-9._\\-]*)*$";
+    private static final String REMOTE_MODULE_PATTERN = "^[a-z0-9][a-z0-9._\\-]*/[a-z][a-z0-9._\\-]*(/[a-z][a-z0-9._\\-]*)*$";
 
     static boolean isRemoteModule(String source) {
         if( source.startsWith("/") || source.startsWith("./") || source.startsWith("../") )
             return false;
         return source.matches(REMOTE_MODULE_PATTERN);
     }
 
-    private static URI getIncludeUri(Path parent, String source) {
+    private static URI getLocalIncludeUri(Path parent, String source) {
         Path includePath = parent.resolve(source);
         if( Files.isDirectory(includePath) )
             includePath = includePath.resolve("main.nf");
diff --git a/modules/nf-lang/src/main/java/nextflow/script/control/ResolveIncludeVisitor.java b/modules/nf-lang/src/main/java/nextflow/script/control/ResolveIncludeVisitor.java
@@ -22,6 +22,7 @@
 import java.util.List;
 import java.util.Set;
 
+import nextflow.module.spi.RemoteModuleResolverProvider;
 import nextflow.script.ast.FunctionNode;
 import nextflow.script.ast.IncludeNode;
 import nextflow.script.ast.ScriptNode;
@@ -48,6 +49,8 @@ public class ResolveIncludeVisitor extends ScriptVisitorSupport {
 
     private URI uri;
 
+    private Path projectDir;
+
     private Compiler compiler;
 
     private Set<URI> changedUris;
@@ -56,15 +59,16 @@ public class ResolveIncludeVisitor extends ScriptVisitorSupport {
 
     private boolean changed;
 
-    public ResolveIncludeVisitor(SourceUnit sourceUnit, Compiler compiler, Set<URI> changedUris) {
+    public ResolveIncludeVisitor(SourceUnit sourceUnit, Path projectDir, Compiler compiler, Set<URI> changedUris) {
         this.sourceUnit = sourceUnit;
         this.uri = sourceUnit.getSource().getURI();
         this.compiler = compiler;
         this.changedUris = changedUris;
+        this.projectDir = projectDir;
     }
 
-    public ResolveIncludeVisitor(SourceUnit sourceUnit, Compiler compiler) {
-        this(sourceUnit, compiler, null);
+    public ResolveIncludeVisitor(SourceUnit sourceUnit, Path projectDir, Compiler compiler) {
+        this(sourceUnit, projectDir, compiler, null);
     }
 
     @Override
@@ -86,9 +90,15 @@ public void visitInclude(IncludeNode node) {
             return;
         }
 
-        var isRemoteModule = ModuleResolver.isRemoteModule(source);
-        var parent = isRemoteModule ? Path.of("modules") : Path.of(uri).getParent();
-        var includeUri = getIncludeUri(parent, source);
+        URI includeUri;
+        try {
+            includeUri = getIncludeUri(source);
+        }
+        catch( Exception e ) {
+            addError(e.getMessage(), node);
+            return;
+        }
+
         if( !isIncludeStale(node, includeUri) )
             return;
         changed = true;
@@ -126,7 +136,20 @@ private static void setPlaceholderTargets(IncludeNode node) {
         }
     }
 
-    private static URI getIncludeUri(Path parent, String source) {
+    private URI getIncludeUri(String source) {
+        if( ModuleResolver.isRemoteModule(source) ) {
+            return RemoteModuleResolverProvider.getInstance()
+                .resolve(source, projectDir)
+                .normalize()
+                .toUri();
+        }
+        else {
+            var parent = Path.of(uri).getParent();
+            return getLocalIncludeUri(parent, source);
+        }
+    }
+
+    private static URI getLocalIncludeUri(Path parent, String source) {
         Path includePath = parent.resolve(source);
         if( Files.isDirectory(includePath) )
             includePath = includePath.resolve("main.nf");
diff --git a/modules/nf-lang/src/main/java/nextflow/script/control/ScriptParser.java b/modules/nf-lang/src/main/java/nextflow/script/control/ScriptParser.java

Original file line number	Diff line number	Diff line change
`@@ -24,5 +24,5 @@ import groovy.transform.InheritConstructors`
`24`	`24`	`* @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>`
`25`	`25`	`*/`
`26`	`26`	`@InheritConstructors`
`27`		`-class IllegalModulePath extends Exception {`
	`27`	`+class IllegalModulePathException extends Exception {`
`28`	`28`	`}`
Original file line number	Diff line number	Diff line change
`@@ -161,7 +161,7 @@ class ModuleResolver {`
`161`	`161`	`// Install to modules directory (will compute directory checksum for future integrity checks)`
`162`	`162`	`InstalledModule installed = storage.installModule(reference, version, tempFile, downloadUrl)`
`163`	`163`
`164`		`- log.info "Module ${reference}@${version} installed successfully at ${installed.mainFile.parent}"`
	`164`	`+ log.info "Module ${reference}@${version} installed successfully at ${installed.mainFile.parent.toAbsolutePath()}"`
`165`	`165`	`return installed.mainFile`
`166`	`166`	`}`
`167`	`167`	`finally {`
Original file line number	Diff line number	Diff line change
`@@ -175,7 +175,7 @@ class ScriptLoaderV2 implements ScriptLoader {`
`175`	`175`
`176`	`176`	`private ScriptCompiler getCompiler() {`
`177`	`177`	`if( !compiler )`
`178`		`- compiler = new ScriptCompiler(session.debug, session.classesDir, session.getClassLoader())`
	`178`	`+ compiler = new ScriptCompiler(session.debug, session.classesDir, session.getClassLoader(), session.baseDir)`
`179`	`179`	`return compiler`
`180`	`180`	`}`
`181`	`181`