Dx green with nf-core/rnaseq

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

@@ -441,6 +441,10 @@ class BashWrapperBuilder {
         throw new IllegalArgumentException("Unknown container engine: $engine")
     }
 
+    protected boolean getAllowContainerMounts() {
+        return true
+    }
+
     /**
      * Build a {@link DockerBuilder} object to handle Docker commands
      *
@@ -458,16 +462,18 @@ class BashWrapperBuilder {
          * initialise the builder
          */
         // do not mount inputs when they are copied in the task work dir -- see #1105
-        if( stageInMode != 'copy' )
+        if( stageInMode != 'copy' && allowContainerMounts )
             builder.addMountForInputs(inputFiles)
 
-        builder.addMount(binDir)
+        if( allowContainerMounts )
+            builder.addMount(binDir)
 
         if(this.containerMount)
             builder.addMount(containerMount)
 
         // task work dir
-        builder.setWorkDir(workDir)
+        if( allowContainerMounts )
+            builder.setWorkDir(workDir)
 
         // set the name
         builder.setName('$NXF_BOXID')

modules/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategy.groovy

@@ -59,7 +59,7 @@ class AwsBatchFileCopyStrategy extends SimpleFileCopyStrategy {
     @Override
     String getEnvScript(Map environment, boolean container) {
         if( container )
-            throw new IllegalArgumentException("Parameter `wrapHandler` not supported by ${this.class.simpleName}")
+            throw new IllegalArgumentException("Parameter `container` not supported by ${this.class.simpleName}")
 
         final result = new StringBuilder()
         final copy = environment ? new HashMap<String,String>(environment) : Collections.<String,String>emptyMap()

modules/nf-amazon/src/test/nextflow/cloud/aws/util/S3PathTest.groovy

@@ -0,0 +1,45 @@
+package nextflow.cloud.aws.util
+
+import nextflow.file.FileHelper
+import spock.lang.Specification
+import spock.lang.Unroll
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class S3PathTest extends Specification {
+
+    @Unroll
+    def 'should convert to uri string' () {
+
+        expect:
+        FileHelper.asPath(PATH).toUriString() == STR
+
+        where:
+        _ | PATH                | STR
+        _ | 's3://foo'          | 's3://foo/'
+        _ | 's3://foo/bar'      | 's3://foo/bar'
+        _ | 's3://foo/b a r'    | 's3://foo/b a r'
+        _ | 's3://f o o/bar'    | 's3://f o o/bar'
+        _ | 's3://f_o_o/bar'    | 's3://f_o_o/bar'
+
+    }
+
+    @Unroll
+    def 'should convert to string' () {
+
+        expect:
+        FileHelper.asPath(PATH).toString() == STR
+
+        where:
+        _ | PATH                | STR
+        _ | 's3://foo'          | '/foo/'
+        _ | 's3://foo/bar'      | '/foo/bar'
+        _ | 's3://foo/b a r'    | '/foo/b a r'
+        _ | 's3://f o o/bar'    | '/f o o/bar'
+        _ | 's3://f_o_o/bar'    | '/f_o_o/bar'
+
+    }
+
+}

modules/nf-commons/src/main/nextflow/extension/FilesEx.groovy

@@ -17,8 +17,7 @@
 
 package nextflow.extension
 
-import org.codehaus.groovy.runtime.InvokerHelper
-import static java.nio.file.StandardCopyOption.REPLACE_EXISTING
+import static java.nio.file.StandardCopyOption.*
 
 import java.nio.ByteBuffer
 import java.nio.channels.SeekableByteChannel
@@ -43,6 +42,7 @@ import groovy.transform.stc.ClosureParams
 import groovy.transform.stc.FromString
 import groovy.util.logging.Slf4j
 import nextflow.file.FileHelper
+import nextflow.file.FileSystemPathFactory
 import nextflow.io.ByteBufferBackedInputStream
 import nextflow.util.CharsetHelper
 import nextflow.util.CheckHelper
@@ -1492,11 +1492,10 @@ class FilesEx {
             return path.toString()
         if( scheme == 's3' )
             return "$scheme:/$path".toString()
-        if( scheme == 'gs' ) {
-            final bucket = InvokerHelper.invokeMethod(path, 'bucket', InvokerHelper.EMPTY_ARGS)
-            return "$scheme://$bucket$path".toString()
-        }
-        return path.toUri().toString()
+        //
+        final result = FileSystemPathFactory.getUriString(path)
+        //
+        return result ?: path.toUri().toString()
     }
 
     static String getScheme(Path path) {

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

@@ -29,10 +29,29 @@ import groovy.transform.Memoized
 @CompileStatic
 abstract class FileSystemPathFactory {
 
+    /**
+     * Converts path uri string to the corresponding {@link Path} object
+     *
+     * @param uri
+     *      A fully qualified path uri including the protocol scheme
+     * @return
+     *      A {@link Path} for the given path or {@code null} if protocol is unknown
+     */
     abstract protected Path parseUri(String uri)
 
+    /**
+     * Converts a {@link Path} object to a fully qualified uri string
+     *
+     * @param path
+     *      The {@link Path} object to be converted
+     * @return
+     *      The uri string corresponding to the specified path or {@code null}
+     *      if the no provider is found
+     */
+    abstract protected String toUriString(Path path)
+
     static Path parse(String uri) {
-        def factories = factories0()
+        final factories = factories0()
         for( int i=0; i<factories.size(); i++ ) {
             final result = factories[i].parseUri(uri)
             if( result )
@@ -41,6 +60,16 @@ abstract class FileSystemPathFactory {
         return null
     }
 
+    static String getUriString(Path path) {
+        final factories = factories0()
+        for( int i=0; i<factories.size(); i++ ) {
+            final result = factories[i].toUriString(path)
+            if( result )
+                return result
+        }
+        return null
+    }
+
     @Memoized
     private static List<FileSystemPathFactory> factories0() {
         final result = new ArrayList(10)

modules/nf-google/src/main/nextflow/cloud/google/util/GsPathFactory.groovy

@@ -20,12 +20,12 @@ import java.nio.file.Path
 
 import com.google.cloud.storage.contrib.nio.CloudStorageConfiguration
 import com.google.cloud.storage.contrib.nio.CloudStorageFileSystem
+import com.google.cloud.storage.contrib.nio.CloudStoragePath
 import groovy.transform.CompileStatic
 import nextflow.Global
 import nextflow.Session
 import nextflow.cloud.google.lifesciences.GoogleLifeSciencesConfig
 import nextflow.file.FileSystemPathFactory
-
 /**
  * Implements FileSystemPathFactory interface for Google storage
  *
@@ -62,4 +62,12 @@ class GsPathFactory extends FileSystemPathFactory {
                 ? CloudStorageFileSystem.forBucket(str, storageConfig).getPath('')
                 : CloudStorageFileSystem.forBucket(str.substring(0,p), storageConfig).getPath(str.substring(p)) )
     }
+
+    @Override
+    protected String toUriString(Path path) {
+        if( path instanceof CloudStoragePath ) {
+            return "gs://${path.bucket()}$path".toString()
+        }
+        return null
+    }
 }

modules/nf-google/src/test/nextflow/cloud/google/util/GsPathFactoryTest.groovy

@@ -36,14 +36,15 @@ class GsPathFactoryTest extends Specification {
 
         expect:
         factory.parseUri(PATH).toUriString() == PATH
+        factory.parseUri(PATH).toString() == STR
 
         where:
-        _ | PATH
-        _ | 'gs://foo'
-        _ | 'gs://foo/bar'
-        _ | 'gs://foo/b a r'
-        _ | 'gs://f o o/bar'
-        _ | 'gs://f_o_o/bar'
+        _ | PATH                | STR
+        _ | 'gs://foo'          | ''
+        _ | 'gs://foo/bar'      | '/bar'
+        _ | 'gs://foo/b a r'    | '/b a r'
+        _ | 'gs://f o o/bar'    | '/bar'
+        _ | 'gs://f_o_o/bar'    | '/bar'
     }
 
     def 'should use requester pays' () {