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Differences Between WDL Versions

⚙️denotes a change that affects the parser

1.1 to development

  • ⚙️ Introduces the Directory type
  • ⚙️ Restricts the runtime section to only the standard attributes
    • container is now a required runtime attribute
  • ⚙️ Adds a hints section for arbitrary runtime hints
  • ⚙️ Removes the Object type and the read_object* and write_object* functions
  • ⚙️ Removes placeholder options (sep, true/false, and default)

1.0 to 1.1

  • ⚙️ Introduces None value for explicitly declaring an optional parameter as undefined.
  • ⚙️ Introduces a new notation for Struct literals
  • The Object type is now deprecated - Structs should be used instead
  • Adds support for relative imports
  • ⚙️ Adds new "pass-through" syntax for call inputs
  • ⚙️ Adds new after keyword for making explicit dependencies between calls
  • Formally defines the standard runtime attributes
    • container is added as an alias of docker - the use of docker is deprecated
    • container now supports image names in URI form (e.g. docker://repo/img:tag) and assumes docker:// by default
  • Added the following new functions to the standard library:
    • min
    • max
    • suffix
    • quote
    • squote
    • keys
    • as_map
    • collect_by_key
    • sep
    • unzip
  • Makes explicit that the sub function supports POSIX Extended Regular Expressions (EREs)
    • Support for other regular expression formats is deprecated
  • Formally defines the JSON input and output formats
    • Includes the ability to override runtime attributes in the input JSON
  • Makes explicit that unsatisified task inputs should not be allowed when running workflows
    • Introduces the allowNestedInputs attribute that can be used in the workflow meta section to explicitly allow unsatisfied task inputs
  • Deprecates:
    • Use of file:// imports
    • Placeholder options (sep, true/false, and default)

Draft-2 to 1.0

  • ⚙️ Version statement required (as of draft-3)
  • ⚙️ Structs
  • ⚙️ For both tasks and workflows, unbound inputs must be within the input {} block
    • Declarations outside input block cannot be overridden
    • As a consequence of this, the way workflow inputs are calculated differs between the two specs - refer to the “Computing Inputs” sections for details
  • The workflow output section is optional in both specs, but the 1.0 spec clarifies that the output section is required in a workflow called as a sub-workflow.
  • Task command section
    • ⚙️ Placeholders can begin with ~ rather than $
    • ⚙️ Placeholders in heredoc-style command (command <<< >>>) may only use the ~{} style placeholder
    • command <<< >>> with ~{} placeholders is strongly preferred to avoid any mis-parsing of bash variables
    • In Draft-2 it was allowed to specify only one of the true/false options in a placeholder - the other option evaluated to empty string. In 1.0, both options are required.
  • meta and parameter_meta are allowed to contain number, boolean, object, or array values in addition to strings
  • Standard library
    • size can be computed for certain compound types

Non-features

These are features that appear in either or both of the Draft-2 and 1.0 specs that are here explicitly specified as non-features i.e. consider these sections of the spec(s) as redlined.

  • Both Draft-2 and 1.0 mention a loop (or while) construct. It appears in both the Draft-2 and 1.0 Hermes grammars. However, I don’t think it was ever supported in Cromwell, and it is dropped in 2.0.
  • ⚙️ Wildcard syntax in the output section in Draft-2 is deprecated, and is dropped in 1.0. Parsers are not required to support this syntax in order to be considered compliant.

Open Questions

These items are ambiguous in either or both of the Draft-2 and 1.0 specs - whether or not they should be considered part of the spec will probably be determined by whether they are implemented in Cromwell.

  • Coercion of Map to Object - 1.0 does support this, but I think Draft-2 does not support this.
  • The Draft-2 spec mentions a quote placeholder option once, but it is never referred to again. The Hermes grammar does not enumerate the allowed options. It is definitely not supported in 1.0.
  • The 1.0 spec says that optional inputs with defaults are allowed, whereas the Draft-2 spec does not say one way or the other.
  • The Draft-2 spec says that an optional variable whose value is unspecified will evaluate to the empty string. The 1.0 spec does not say how a variable with an unspecified value is evaluated - I am guessing it is an error?

References