diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index daa686b878..213319c02f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -630,7 +630,7 @@ class CmdRun extends CmdBase implements HubOptions {
         /*
          * try to look for a pipeline in the repository
          */
-        def manager = new AssetManager(pipelineName, this)
+        def manager = new AssetManager(pipelineName, mainScript, this)
         def repo = manager.getProject()
 
         boolean checkForUpdate = true
diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
index b35f1a06d2..75fc112aab 100644
--- a/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
@@ -106,6 +106,14 @@ class AssetManager {
         build(pipelineName, config, cliOpts)
     }
 
+    AssetManager( String pipelineName, String scriptFile, HubOptions cliOpts = null) {
+        assert pipelineName
+        // read the default config file (if available)
+        def config = ProviderConfig.getDefault()
+        // build the object
+        build(pipelineName, config, cliOpts, scriptFile)
+    }
+
     AssetManager( String pipelineName, Map config ) {
         assert pipelineName
         // build the object
@@ -121,10 +129,11 @@ class AssetManager {
      * @return The {@link AssetManager} object itself
      */
     @PackageScope
-    AssetManager build( String pipelineName, Map config = null, HubOptions cliOpts = null ) {
+    AssetManager build( String pipelineName, Map config = null, HubOptions cliOpts = null, String scriptFile = null) {
 
         this.providerConfigs = ProviderConfig.createFromMap(config)
-
+        if( scriptFile )
+            this.mainScript = scriptFile
         this.project = resolveName(pipelineName)
         this.localPath = checkProjectDir(project)
         this.hub = checkHubProvider(cliOpts)
@@ -311,6 +320,9 @@ class AssetManager {
         if( !isUrl )
             return null
 
+        if( repository.endsWith('.nf') || repository.endsWith('.nxf') )
+            throw new AbortOperationException("Repository URL can end as a script file (.nf|.nxf) - Use -main-script option.")
+
         try {
             def url = new GitUrl(repository)