Fix remote modules when base dir is not the current working dir

modules/nextflow/src/main/groovy/nextflow/module/DefaultRemoteModuleResolver.groovy

@@ -45,8 +45,8 @@ import java.nio.file.Path
 class DefaultRemoteModuleResolver implements RemoteModuleResolver {
 
     @Override
-    Path resolve(String moduleName, Path baseDir) {
-
+    Path resolve(String moduleName) {
+        def baseDir = Global.session?.baseDir ?: Path.of('.').toAbsolutePath()
         final config = Global.config ?: new ConfigBuilder().setBaseDir(baseDir).build()
         final registryConfig = config.navigate('registry') as RegistryConfig
 

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 {

modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy

@@ -181,7 +181,7 @@ class IncludeDef {
     Path resolveRemoteModulePath(String moduleName) {
         // Use SPI to get the remote module resolver implementation
         def resolver = RemoteModuleResolverProvider.getInstance()
-        return resolver.resolve(moduleName, session.baseDir)
+        return resolver.resolve(moduleName)
     }
 
     @PackageScope

modules/nf-lang/src/main/java/nextflow/module/spi/FallbackRemoteModuleResolver.java

@@ -31,7 +31,11 @@
 public class FallbackRemoteModuleResolver implements RemoteModuleResolver {
 
     @Override
-    public Path resolve(String moduleName, Path baseDir) {
+    public Path resolve(String moduleName) {
+        // Use CWD-relative "modules" directory as a best-effort fallback when no
+        // RemoteModuleResolver SPI implementation is available (e.g. running outside
+        // a full Nextflow session).
+        final Path baseDir = Path.of("modules").toAbsolutePath();
         final var resolved = baseDir.resolve(moduleName).normalize();
         // Prevent path traversal outside the base directory
         if (!resolved.startsWith(baseDir.normalize())) {
@@ -47,4 +51,4 @@ public Path resolve(String moduleName, Path baseDir) {
     public int getPriority() {
         return Integer.MIN_VALUE;  // Fallback has lowest possible priority
     }
-}
+}

modules/nf-lang/src/main/java/nextflow/module/spi/RemoteModuleResolver.java

@@ -47,11 +47,10 @@ 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)
      * @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);
 
     /**
      * Get the priority of this resolver. Higher priority resolvers are tried first.
@@ -65,4 +64,4 @@ public interface RemoteModuleResolver {
     default int getPriority() {
         return 0;
     }
-}
+}

modules/nf-lang/src/main/java/nextflow/script/control/ModuleResolver.java

@@ -74,17 +74,9 @@ 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 includeUri = isRemoteModule(source) ?
+            RemoteModuleResolverProvider.getInstance().resolve(source).normalize().toUri() :
+            getIncludeUri(Path.of(sourceUnit.getSource().getURI()).getParent(), source);
         if( compiler.getSource(includeUri) != null )
             return null;
         if( !Files.exists(Path.of(includeUri)) )

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;
@@ -86,9 +87,19 @@ 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;
+        if( ModuleResolver.isRemoteModule(source) ) {
+            try {
+                includeUri = RemoteModuleResolverProvider.getInstance().resolve(source).normalize().toUri();
+            }
+            catch( IllegalStateException e ) {
+                addError(e.getMessage(), node);
+                return;
+            }
+        }
+        else {
+            includeUri = getIncludeUri(Path.of(sourceUnit.getSource().getURI()).getParent(), source);
+        }
         if( !isIncludeStale(node, includeUri) )
             return;
         changed = true;