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

The wdlTools.syntax package implements an abstract syntax tree (AST) for WDL. It uses the OpenWDL Antlr4 grammar originally created by Patrick Magee.

Currently, WDL draft-2, 1.0, 1.1, and development/2.0 are fully supported (with some limitations).

import wdlTools.syntax.AbstractSyntax._
import wdlTools.syntax.Parsers
import dx.util.{FileNode, FileSourceResolver}
val parsers = Parsers(followImports = true)
val wdl: FileNode = 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}")
}

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 "beta" quality - please report any bugs/enhancements using the issue tracker.

• check: type-check a WDL file
• docgen: generate documentation for WDL tasks/workflows
• exec: execute a WDL task (workflow execution is not yet supported)
• fix: attempts to fix non-standard WDL files with specification incompatibilities
• format: reformat a WDL file
  • Note: draft-2 is not yet supported.
• lint: detect "lint" (i.e. incorrect style or potentially problematic code) in a WDL file
  • Note: this command is not yet full-featured. You may want to also use miniwdl lint.
• 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 dxCompiler
• upgrade: upgrade a WDL file to a newer version; currently only draft-2 -> [1.0, 1.1] is supported

• Forward references are not yet supported, i.e. a variable must be declared before it is referenced
• Incomplete linter rules
• Runtime and hint attributes cannot be overriden at runtime in the task runner

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-4.9-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.

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.