Include support for git-remote-s3

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

@@ -324,6 +324,7 @@ class CmdRun extends CmdBase implements HubOptions {
         printBanner()
 
         // -- resolve main script
+        Plugins.init()
         final scriptFile = getScriptFile(pipeline)
 
         // -- load command line params
@@ -359,7 +360,6 @@ class CmdRun extends CmdBase implements HubOptions {
         Map configParams = builder.getConfigParams()
 
         // -- Load plugins (may register secret providers)
-        Plugins.init()
         Plugins.load(config)
 
         // -- Initialize real secrets system

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

@@ -100,6 +100,7 @@ class Launcher {
                 new CmdList(),
                 new CmdLog(),
                 new CmdPull(),
+                new CmdPush(),
                 new CmdRun(),
                 new CmdKubeRun(),
                 new CmdDrop(),

modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy

@@ -112,6 +112,14 @@ class AssetManager {
         build(pipelineName, config)
     }
 
+    AssetManager(File path, String pipelineName, HubOptions cliOpts = null ) {
+        assert path
+        assert pipelineName
+        // build the object
+        def config = ProviderConfig.getDefault()
+        build(path, pipelineName, config, cliOpts)
+    }
+
     /**
      * Build the asset manager internal data structure
      *
@@ -135,6 +143,22 @@ class AssetManager {
         return this
     }
 
+    @PackageScope
+    AssetManager build( File path, String pipelineName, Map config = null, HubOptions cliOpts = null ) {
+
+        this.providerConfigs = ProviderConfig.createFromMap(config)
+
+        this.project = resolveName(pipelineName)
+        this.localPath = path
+        this.hub = checkHubProvider(cliOpts)
+        this.provider = createHubProvider(hub)
+        setupCredentials(cliOpts)
+        validateProjectDir()
+
+        return this
+    }
+
+
     @PackageScope
     File getLocalGitConfig() {
         localPath ? new File(localPath,'.git/config') : null
@@ -307,7 +331,7 @@ class AssetManager {
     @PackageScope
     String resolveNameFromGitUrl( String repository ) {
 
-        final isUrl = repository.startsWith('http://') || repository.startsWith('https://') || repository.startsWith('file:/')
+        final isUrl = repository.startsWith('http://') || repository.startsWith('https://') || repository.startsWith('file:/') || repository.startsWith('s3://')
         if( !isUrl )
             return null
 
@@ -685,6 +709,45 @@ class AssetManager {
 
     }
 
+    /**
+     * Upload a pipeline to a remote repository
+     *
+     * @param revision The revision/branch to upload
+     * @param remoteName The name of the remote (default: origin)
+     * @param isNewRepo Whether this is a new repository initialization
+     * @result A message representing the operation result
+     */
+    String upload(String revision, String remoteName = "origin", boolean isNewRepo = false) {
+        assert project
+        assert localPath
+
+        // Create and checkout branch if it doesn't exist
+        try {
+            git.checkout().setName(revision).call()
+        }
+        catch( Exception ignored ) {
+            // Branch doesn't exist, create it
+            git.checkout()
+                .setCreateBranch(true)
+                .setName(revision)
+                .call()
+        }
+
+
+        def pushCommand = git.push()
+            .setRemote(remoteName)
+
+        pushCommand.add(revision)
+
+        if( provider.hasCredentials() )
+            pushCommand.setCredentialsProvider( provider.getGitCredentials() )
+
+        def result = pushCommand.call()
+        return "pushed to ${remoteName} (${revision})"
+    }
+
+
+
     /**
      * Clone a pipeline from a remote pipeline repository to the specified folder
      *

modules/nextflow/src/main/groovy/nextflow/scm/RepositoryFactory.groovy

@@ -88,6 +88,7 @@ class RepositoryFactory implements ExtensionPoint {
 
     // --==  static definitions ==--
     private static boolean codeCommitLoaded
+    private static boolean s3Loaded
     private static List<RepositoryFactory> factories0
 
     private static List<RepositoryFactory> factories() {
@@ -102,6 +103,11 @@ class RepositoryFactory implements ExtensionPoint {
 
     static RepositoryProvider newRepositoryProvider(ProviderConfig config, String project) {
         // check if it's needed to load new plugins
+        if( config.platform == 's3' && !s3Loaded){
+            Plugins.startIfMissing('nf-amazon')
+            s3Loaded=true
+            factories0=null
+        }
         if( (config.name=='codecommit' || config.platform=='codecommit') && !codeCommitLoaded ) {
             Plugins.startIfMissing('nf-codecommit')
             codeCommitLoaded=true
@@ -120,6 +126,11 @@ class RepositoryFactory implements ExtensionPoint {
 
     static ProviderConfig newProviderConfig(String name, Map<String,Object> attrs) {
         // check if it's needed to load new plugins
+        if( attrs.platform == 's3' && !s3Loaded){
+            Plugins.startIfMissing('nf-amazon')
+            s3Loaded=true
+            factories0=null
+        }
         if( (name=='codecommit' || attrs.platform=='codecommit') && !codeCommitLoaded ) {
             Plugins.startIfMissing('nf-codecommit')
             codeCommitLoaded=true
@@ -134,6 +145,11 @@ class RepositoryFactory implements ExtensionPoint {
     }
 
     static ProviderConfig getProviderConfig(List<ProviderConfig> providers, GitUrl url) {
+        if( url.protocol.equals('s3') && !s3Loaded){
+            Plugins.startIfMissing('nf-amazon')
+            s3Loaded=true
+            factories0=null
+        }
         if( url.domain.startsWith('git-codecommit.') && url.domain.endsWith('.amazonaws.com') && !codeCommitLoaded ) {
             Plugins.startIfMissing('nf-codecommit')
             codeCommitLoaded=true