rhpvorderman / wdltools

WDL tools for parsing, type-checking, and more

WDL Scala Tools

Scala programming language library for parsing WDL, and command-line tools for type-checking, code formatting, and more.

Abstract Syntax Tree (AST)

The wdlTools.syntax package implements an abstract syntax tree (AST) for WDL. It uses Antlr4 grammar developed by Patrick Magee. The class definitions reside in src/main/scala/wdlTools/syntax/AbstractSyntax.scala.

Currently, WDL draft-2 and 1.0 are fully supported, and development/2.0 is partially supported.

import wdlTools.syntax.AbstractSyntax._
import wdlTools.syntax.Parsers
import wdlTools.util.{FileSource, FileSourceResolver}
val parsers = Parsers(followImports = true)
val wdl: FileSource = FileSourceResolver.get.resolve("file:///path/to/my/wdl")
val doc: Document = parsers.parseDocument(wdl)
// print the source locations of all tasks in the document
doc.elements.foreach {
  case task: Task => println(s"Task ${task.name} is at ${task.loc}")
}

Command line tools

The wdlTools JAR also provides various command line tools to accelerate and simplify the development of WDL workflows. You can get help by running:

$ java -jar wdlTools.jar [command] --help

The following commands are currently available. They should be considered "alpha" quality - please report any bugs/enhancements using the issue tracker.

• check: type-check a WDL file
• docgen: generate documentation for WDL tasks/workflows
• format: reformat a WDL file
• lint: detect "lint" (i.e. incorrect style or potentially problematic code) in a WDL file
• new: generate a new WDL project
• printTree: print the Abstract Syntax Tree for a WDL document
• readmes: generate README files for the tasks/workflows in a WDL file - these files are named so that they will be recognized when building DNAnexus apps/workflows using dxWDL
• upgrade: upgrade a WDL file to a newer version; currently only draft-2 -> 1.0 is supported

Building

The java code for the parser is generated by the ANTRL4 tool.

1. Download a jar file with the instructions
2. cd GIT_REPO
3. Assuming you downloaded the jar file to $HOME/antlr-4.8-complete.jar generated java code from the grammar by running make from the toplevel.
4. Build the scala code:

   sbt compile
   

5. Run the tests:

   sbt test
   

See the documentation for full details.

Support

wdlTools is not an official product of DNAnexus. Please do not contact DNAnexus (or any employees thereof) for support. To report a bug or feature request, please open an issue in the issue tracker.