Bump JGit 6.5 and use depth 1 when cloning repos

Signed-off-by: Alexander Stram <[email protected]>

Author: ahstram

modules/nextflow/build.gradle

@@ -35,7 +35,7 @@ dependencies {
     api "com.beust:jcommander:1.35"
     api("com.esotericsoftware.kryo:kryo:2.24.0") { exclude group: 'com.esotericsoftware.minlog', module: 'minlog' }
     api('org.iq80.leveldb:leveldb:0.12')
-    api('org.eclipse.jgit:org.eclipse.jgit:6.2.0.202206071550-r')
+    api('org.eclipse.jgit:org.eclipse.jgit:6.5.0.202303070854-r')
     api ('javax.activation:activation:1.1.1')
     api ('javax.mail:mail:1.4.7')
     api ('org.yaml:snakeyaml:2.0')

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

@@ -594,6 +594,7 @@ class AssetManager {
             clone
                 .setURI(cloneURL)
                 .setDirectory(localPath)
+                .setDepth(1)
                 .setCloneSubmodules(manifest.recurseSubmodules)
                 .call()
 
@@ -674,6 +675,7 @@ class AssetManager {
 
         clone.setURI(uri)
         clone.setDirectory(directory)
+        clone.setDepth(1)
         clone.setCloneSubmodules(manifest.recurseSubmodules)
         if( provider.hasCredentials() )
             clone.setCredentialsProvider( provider.getGitCredentials() )