dnanexus/dxCompiler 2.6.0

dxCompiler 2.6.0

on GitHub

• Implements Directory support for CWL and for WDL development/2.0
• Implements CWL secondaryFiles support
• Implements CWL workflow support
• Breaking Change: the inputs folder is now modified to be read-only for non-streaming files (this has always been the case for streaming files). This means that tasks that create files in the inputs folder will no longer work. For example, a task that creates an index file in place for an input BAM file should be changed from:

  command <<<
  samtools index ~{mybam}
  >>>

  to

  command <<<
  mkdir bams
  ln -s ~{mybam} bams/~{basename(mybam)}
  samtools index bams/~{basename(mybam)}
  >>>

Dependency updates

wdlTools 0.17.1

• Fixes parsing of placeholder options in draft-2 and 1.0 such that default and sep are no longer treated as reserved words

cwlScala 0.7.0

• Breaking Change: Sink.linkMerge is now Optional
• Introduces ParserResult class, which is returned from all Parser.parse* methods
• For packed workflows, parses out $schemas and $namespaces
• Updates to latest cwljava, which fixes several parsing errors
• Fixes CwlType.flatten to correctly handle duplicate types
• Treats scatter sources as identifiers
• Automatically renames the main process if its name collides with another process
• Fixes evalution of compound parameter references
• Set CommandLineTool.successCodes to Set(0) if not specified
• Fixes deserialization of optional fields
• Uses the source file name as the process name when processing a $graph where the top-level element ID is 'main'
• Fixes evaluation for Directory-type values with listings
• Fixes parsing of LoadListingEnum values
• Adds option to Parser.parseFile and Parser.parseString to specify that the CWL file is in "packed" form
• Updates to latest cwljava, which fixes parsing of anonymous schemas in packed documents
• Correctly handles identifiers with namespaces from imported documents
• Fixes error when trying to finalize a File value without location or path
• Updates dxCommon to 0.2.15-SNAPSHOT
• Uses FileSource.listing to determine directory listing during finalization
• Updates to dxCommon 0.7.0
• Breaking change: schema types now have id: Option[Identifier] rather than name: Option[String]
• Parser can now handle $graph style CWL documents
• Adds dependency on dxCommon library
• Improves finalization of file values
• Fixes coercion of StringValue to CwlEnum
• other bugfixes
• Adds EvaluatorContext.createInputs to create an EvaluatorContext from input values
• Performs "finalization" of input values (setting of missing attributes on File and Directory values) when using EvaluatorContext.createInputs or EvaluatorContext.createStaticInputs
• Parser bugfixes
• Incorporate cwljava/39, which fixes workflow parsing issues
• Allow duplicate Requirements/Hints and specify priority rules
• Breaking change: added new CwlMulti type and removed all uses of Vector[CwlType]