Add recursive options to nextflow run/clone/pull commands

nextflow-io · Jun 9, 2020 · 8447dfd · 8447dfd
1 parent 8f475f4
commit 8447dfd
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Showing 4 changed files with 23 additions and 11 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdClone.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdClone.groovy
@@ -39,6 +39,9 @@ class CmdClone extends CmdBase implements HubOptions {
     @Parameter(names='-r', description = 'Revision to clone - It can be a git branch, tag or revision number')
     String revision
 
+    @Parameter(names=['-recursive','-recurse-submodules'], description = 'initialize submodules in the clone', arity = 0)
+    boolean recurse_submodules
+
     @Override
     final String getName() { NAME }
 
@@ -63,7 +66,7 @@ class CmdClone extends CmdBase implements HubOptions {
 
         manager.checkValidRemoteRepo()
         print "Cloning ${manager.project}${revision ? ':'+revision:''} ..."
-        manager.clone(target, revision)
+        manager.clone(target, revision, recurse_submodules)
         print "\r"
         println "${manager.project} cloned to: $target"
     }

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdPull.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdPull.groovy
@@ -42,6 +42,8 @@ class CmdPull extends CmdBase implements HubOptions {
     @Parameter(names=['-r','-revision'], description = 'Revision of the project to run (either a git branch, tag or commit SHA number)')
     String revision
 
+    @Parameter(names='-recursive', description = 'control recursive fetching of submodules', arity = 0)
+    boolean recurse_submodules
 
 
     @Override
@@ -71,8 +73,8 @@ class CmdPull extends CmdBase implements HubOptions {
             log.info "Checking $it ..."
             def manager = new AssetManager(it, this)
 
-            def result = manager.download(revision)
-            manager.updateModules()
+            def result = manager.download(recurse_submodules, revision)
+            manager.updateModules(recurse_submodules)
 
             def scriptFile = manager.getScriptFile()
             String message = !result ? " done" : " $result"

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -101,6 +101,9 @@ class CmdRun extends CmdBase implements HubOptions {
     @Parameter(names=['-bucket-dir'], description = 'Remote bucket where intermediate result files are stored')
     String bucketDir
 
+    @Parameter(names=['-recursive','-recurse-submodules'], description = 'Try to download submodules recursively if those do not exist', arity = 0)
+    boolean recurse_submodules
+
     /**
      * Defines the parameters to be passed to the pipeline script
      */
@@ -336,15 +339,15 @@ class CmdRun extends CmdBase implements HubOptions {
             if( offline )
                 throw new AbortOperationException("Unknown project `$repo` -- NOTE: automatic download from remote repositories is disabled")
             log.info "Pulling $repo ..."
-            def result = manager.download()
+            def result = manager.download(recurse_submodules)
             if( result )
                 log.info " $result"
             checkForUpdate = false
         }
         // checkout requested revision
         try {
             manager.checkout(revision)
-            manager.updateModules()
+            manager.updateModules(recurse_submodules)
             def scriptFile = manager.getScriptFile()
             log.info "Launching `$repo` [$runName] - revision: ${scriptFile.revisionInfo}"
             if( checkForUpdate && !offline )

diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
@@ -565,7 +565,7 @@ class AssetManager {
      * @param revision The revision to download
      * @result A message representing the operation result
      */
-    def download(String revision=null) {
+    def download(boolean recurse_submodules = false, String revision=null) {
         assert project
 
         /*
@@ -591,7 +591,7 @@ class AssetManager {
             clone
                 .setURI(cloneURL)
                 .setDirectory(localPath)
-                .setCloneSubmodules(true)
+                .setCloneSubmodules(recurse_submodules)
                 .call()
 
             // return status message
@@ -652,7 +652,7 @@ class AssetManager {
      * @param directory The folder when the pipeline will be cloned
      * @param revision The revision to be cloned. It can be a branch, tag, or git revision number
      */
-    void clone(File directory, String revision = null) {
+    void clone(File directory, String revision = null, boolean recurse_submodules) {
 
         def clone = Git.cloneRepository()
         def uri = getGitRepositoryUrl()
@@ -663,7 +663,7 @@ class AssetManager {
 
         clone.setURI(uri)
         clone.setDirectory(directory)
-        clone.setCloneSubmodules(true)
+        clone.setCloneSubmodules(recurse_submodules)
         if( provider.hasCredentials() )
             clone.setCredentialsProvider(new UsernamePasswordCredentialsProvider(provider.user, provider.password))
 
@@ -939,7 +939,7 @@ class AssetManager {
 
     }
 
-    void updateModules() {
+    void updateModules(boolean recurse_submodules ) {
 
         if( !localPath )
             return // nothing to do
@@ -963,7 +963,11 @@ class AssetManager {
 
         final init = git.submoduleInit()
         final update = git.submoduleUpdate()
-        update.setStrategy(MergeStrategy.RECURSIVE)
+
+        if (recurse_submodules) {
+            update.setStrategy(MergeStrategy.RECURSIVE)
+        }
+
         filter.each { String m -> init.addPath(m); update.addPath(m) }
         // call submodule init
         init.call()