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Changelog

version 1.3.0

  • Clarified that relative paths in File and Directory declarations are resolved relative to the WDL document's parent directory outside the output section, and relative to the task's execution directory inside the output section. Also clarified that optional files evaluate to None in both contexts if the path does not exist. (#735)

  • Added previous to the task variable, enabling runtime access to the previous attempt's computed requirements (#734).

  • Added max_retries to the task variable (#733).

  • Introduced the split standard library function (#729).

  • Documents may now load any document with the same major version and a minor version that is less than or equal to that document's version (#698).

  • Added enumeration types (enum) that define closed sets of named variants with associated values. Enums support explicit and implicit typing, and variant values can be of any WDL type including primitives, compound types, and user-defined types. (#695)

  • Added value() standard library function to extract the inner value from an enum variant. (#695)

version 1.2.1

  • Clarified that task.return_code is only available in the output section, where it has type Int rather than Int? (#742).

  • Updates the compliance suite to use spectool (#752).

  • Formalize replacement string syntax for sub() function to specify backreference support (\1 through \9). (#749).

  • Clarify File and Directory path canonicalization, validation, and equality semantics. Clarify when Files and Directories must exist (at declaration evaluation time, not access time). Add Directory comparison operators to binary operators table (#748).

  • Clarify that File values cannot refer to directories and Directory values cannot refer to files; attempting to assign the wrong type of path is an error (#748).

  • Update join_paths function: change return type from File to String (since the result can be either a file or directory path), and change first argument from File to Directory for the first two overloads (#748).

  • Fix change_extension_task.wdl example to use string interpolation when passing File to sub() function (#747).

  • Clarified that when a Directory is converted to a String, the resulting string does not have a trailing slash (#745).

  • Clarified symlink handling behavior in the glob function (#744).

  • Clarified the restriction on multi-level optionals in the "Optional Types" section. (#743)

  • Clarified that relative paths in File and Directory declarations are resolved relative to the WDL document's parent directory outside the output section, and relative to the task's execution directory inside the output section. Also clarified that optional files evaluate to None in both contexts if the path does not exist. (#735)

  • Clarify that disks mount points ephemeral and should not already exist

  • Deprecate the use of relative path literals in input and private variable declarations.

  • Include fixes to examples introduced in v1.1.3

  • Include fixes to examples that don't compile in wdl-tests (#707, #708, #701, #738, #731, #740, #739). Thanks to @adamnovak and @claymcleod!

  • Add in CI/CD for Miniwdl, Sprocket, Toil and Cromwell for spec compliance.

  • Remove Advanced Task Examples to clearly distinguish what is the testing is in scope. (#730)

version 1.2.0

  • Introduced the concept of "scoped types" to support the use of object-like values within the hints section while still keeping the Object type as deprecated.

  • Added new task requirements and hints sections (#540 and #541), and deprecated the runtime section

  • Added new workflow hints section (#543), and moved allowNestedInputs from workflow meta to hints

  • Deprecated the previously allowed behavior implied by setting allowNestedInputs: true where required task/subworkflow inputs could be left unsatisfied. Now all inputs either need to have a default value or have their value specified in the call inputs. Only optional task/subworkflow inputs that are not explicitly set in the call inputs may have their value set at runtime if the allow_nested_inputs hint is true.

  • Added the ability to access the actual values of requirements, meta, and parameter_meta at runtime.

  • Added fpga requirement and reserved hint for requesting FPGA resources.

  • Added disks and gpu reserved hints for requesting specific resources.

  • Added contains_key function to standard library. PR 603

  • Added exponentiation operator (**).

  • Added find, and matches functions.

  • Added chunk function for chunking an array into sub-arrays.

  • Add parameter_meta section to struct definition.

  • Relaxed the requirements on coercing object/map to struct - extra keys are allowed and ignored. Note that this may constitute a breaking change if you rely on a task to fail when coercing an object/map with extra keys.

  • Added join_paths function to join two or more paths.

  • Added allowance for conversion between Struct types when certain criteria are met.

  • Generalized size function to take any compound value.

  • Added optional default parameter to select_first.

  • Generalized length function to also accept Map, Object, and String arguments.

  • Added multi-line strings. PR 602

  • Added the Array[String] keys(Struct|Object) function variant for getting the member names for a struct or object.

  • Added values function for getting the values from a Map.

  • Added parameters to read_tsv that enable it to read field names from a header row or an Array[String] and return an Array[Object]. PR 627

  • Added contains function for determining whether an array contains a specified value.

  • Clarify how inputs with defaults are implicitly optional PR 464 by @mlin

  • Make input: optional in call bodies. PR 524 by @mlin.

  • Added Directory type. PR 641

  • Added clarification that input files and directories should be treated as read-only. PR 642

  • Added JSON extended file/directory input/output format. [PR 643] (#643)

  • Clarified that local paths are always used when evaluating input/private/command expressions.

  • Clarified the meaning of a remote parent folder for the purposes of localization.

  • Clarified that accessing a non-existent member of an object, struct, or call is an error.

version 1.1.3

  • Fix issues with examples (#653, #654, #661, #662, #663, #664, #666, #667, #668). Thanks to @stxue1!

version 1.1.2

  • State that Union is also the type of some runtime attributes.

  • Remove some syntax sections that were missed in 1.1.1.

  • Clarify short-circuiting of boolean expressions (#199)

  • Added requirement for tests to the RFC

  • Clarifies number of sections allowed within task and workflow blocks. PR 598 by @claymcleod

  • Clarified that read_bool is case-insensitive, and added an example.

version 1.1.1

  • Applied Errata to the 1.1.0 spec.

  • Updated most examples to adhere to the new specification for WDL tests.

  • Added missing File and version keywords to the list of reserved words.

  • Added new sections or materially expanded existing sections:

    • "Limited exceptions" to type coercion rules
    • "Static Analysis and Dynamic Evaluation"
    • "Task Input Localization"
    • "Expression Placeholders" under "Command Section"
    • Hidden types

  • Reformatted all tables.

  • Reorganzied the standard library.

  • Provided codespell configuration and workflow to catch typos. PR 530 by @yarikoptic.

  • Fixed typos, thanks to @yarikoptic, @sejyoti, @mmterpstra, @j23414, @jdavcs, @beukueb, @notestaff, @alberto-mg, @mperf!

version 1.1.0

  • Added Errata.

  • Clarified that the sub function requires a POSIX Extended Regular Expression (ERE). PR 243 by @rhpvorderman

  • Added syntax for struct literals. PR 297 by @patmagee

  • Added engine functions for min and max. PR 304 by @pshapiro

  • Added section on file outputs including optional outputs. PR 310 by @jtratner

  • Added reserved keys, explicit formats, and default values for runtime attributes and hints. PR 315 by @patmagee

  • Namespacing has been clarified. PR 340 by @DavyCats

  • Abbreviated syntax for call inputs bound to workflow-scoped values by name: {input: x, y=b, z} is shorthand for {input: x=x, y=b, z=z} PR 365 by @mlin

  • Write a specification for unsatisfied task inputs and nested optional inputs. PR 359 by @rhpvorderman

  • Adds an engine function for joining arrays of strings. PR 229 and PR 368 by @EvanTheB and @illusional.

  • Added an engine function for adding a suffix to an array of primitives as well as well as quote and squote engine functions. PR 362 @patmagee

  • Added a required input and output format for workflow engines. PR 357

  • The input specification has been clarified. PR 314 by @geoffjentry.

  • Added a list of keywords that can not be used as identifiers. PR 307 by @mlin.

  • Empty call blocks have been clarified. PR 302 by @aednichols.

  • Optional and non-empty type constraints have been clarified. PR 290 by @mlin.

  • The way comments work has been clarified. PR 277 by @patmagee.

  • Implement string escapes in the Hermes grammar. PR 272 by @cjllanwarne.

  • Added None for explicitly stating that an optional variable is not defined. PR 263 by @rhpvorderman.

  • Backported to 1.0: Fix a bug in the grammar regarding unescaped strings. PR 253 and PR 255 by @aednichols.

  • WDL Files should be encoded in UTF-8 now. String definitions have been clarfied. PR 247 by @EvanTheB.

  • The version statement can now be the first non-comment statement. So it can be stated below a license header for example. PR 245 by @ffinfo.

  • Added a keys function to get an array of keys from a map. PR 244 by @ffinfo.

  • Several bugs in the grammar have been fixed. PR 238 and PR 240 by @cjllanwarne.

  • Type conversions and meanings have been clarified. PR 235 by @EvanTheB.

  • Backported to 1.0: Imports are now relative to their current location. PR 220 by @geoffjentry.

  • Added conversion functions as_pairs and as_map to convert between Array[Pair[X,Y]] and Map[X,Y]. PR 219 by @DavyCats.

  • Add an after keyword to run a task after other tasks. PR 162 by @cjllanwarne.

version 1.0.0

  • Rename lexer to WdlV1Lexer
  • Rename parser to WdlV1Parser
  • Rename WdlComments channel to COMMENTS
  • Remove SkipChannel
  • Rename COMMENT -> LINE_COMMENT, emit comments to COMMENTS channel
  • Add Meta mode for parsing meta sections
  • Parse whitespace between command and opening {/<<< within Command mode, so that it is emitted to the HIDDEN channel
  • Ignore trailing commas
  • Formatting -
    • use two spaces always for indentation
    • always wrap statements (i.e. always put opening ':' and closing ';' on newlines)
    • always use PascalCase for tokens within lexer modes

draft-2

  • Added ANTLR4 grammar