Mount pwd in the container when work dir is a symlink

Signed-off-by: Paolo Di Tommaso <[email protected]>

modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy

@@ -28,6 +28,7 @@ import nextflow.container.ContainerBuilder
 import nextflow.container.DockerBuilder
 import nextflow.container.SingularityBuilder
 import nextflow.exception.ProcessException
+import nextflow.file.FileHelper
 import nextflow.processor.TaskBean
 import nextflow.processor.TaskProcessor
 import nextflow.processor.TaskRun
@@ -562,7 +563,7 @@ class BashWrapperBuilder {
         // The current work directory should be mounted only when
         // the task is executed in a temporary scratch directory (ie changeDir != null)
         // See https://github.com/nextflow-io/nextflow/issues/1710
-        builder.addMountWorkDir( changeDir as boolean )
+        builder.addMountWorkDir( changeDir as boolean || FileHelper.getWorkDirIsSymlink() )
 
         builder.build()
         return builder

modules/nf-commons/src/main/nextflow/file/FileHelper.groovy

@@ -428,6 +428,31 @@ class FileHelper {
         isPathNFS(Global.session.workDir)
     }
 
+    /**
+     * @return
+     *      {@code true} when the current session working directory is a symlink path
+     *      {@code false otherwise}
+     */
+    static boolean getWorkDirIsSymlink() {
+        isPathSymlink(Global.session.workDir)
+    }
+
+    @Memoized
+    static boolean isPathSymlink(Path path) {
+        if( path.fileSystem!=FileSystems.default )
+            return false
+        try {
+            return path != path.toRealPath()
+        }
+        catch (NoSuchFileException e) {
+            return false
+        }
+        catch (IOException e) {
+            log.debug "Unable to determine symlink status for path: $path - cause: ${e.message}"
+            return false
+        }
+    }
+
     /**
      * Experimental. Check if a file exists making a second try on NFS mount
      * to avoid false negative.

modules/nf-commons/src/test/nextflow/file/FileHelperTest.groovy

@@ -983,4 +983,24 @@ class FileHelperTest extends Specification {
         [:]                             | [:]                   | [max_error_retry: '5']
     }
 
+    def 'should check symlink status'() {
+        given:
+        def folder = Files.createTempDirectory('test')
+        def dirReal = folder.resolve('x/y/z'); dirReal.mkdirs()
+        def link = Files.createSymbolicLink(folder.resolve('link'), folder.resolve('x'))
+
+        expect:
+        !FileHelper.isPathSymlink(Path.of('/bin'))
+        !FileHelper.isPathSymlink(Path.of('/unknown'))
+        and:
+        Files.exists(link)
+        Files.isSymbolicLink(link)
+        FileHelper.isPathSymlink(link)
+        and:
+        Files.exists(link.resolve('y/z'))
+        FileHelper.isPathSymlink(link.resolve('y/z'))
+
+        cleanup:
+        folder?.deleteDir()
+    }
 }