Codestin Search App

New value type V_ForcedNull is used to avoid an addition of an explicit null input to an Optional value. Previously,
if a task was wrapped in a frag - in some cases Optionals without a value were forced to be an explicit null. This version
fixes such behavior.
Draft-2 parser. Previous behavior: if version is not declared, it is assumed to be draft-2, which has no formal
input definitions for tasks and workflows. However, if a user forgets to declare the version while working on workflow
of a version greater than draft-2 with formal definition of input, the parser fails to follow the syntax and throws
the errors not related to the version or the formatting of the input section. Here this behavior is fixed: if version
is not detected and draft-2 is assumed, we check if the input section is defined and throw an exception in this case.

Optional types are preserved when using outputs from the standard library functions without explicit declaration.

Keep the docker container after a task finishes running, so users can debug docker related job failures.

Runtime object is aware if it was created with default system requirements (Runtime.isDefaultSystemRequirements)

TAT.Workflow has a source attribute in analogy to TAT.Document to be used for checksum calculation for App/Job reuse
Fixes evaluation of structs as input parameters of workflow/scatter: hash inputs are coerced from object to struct, and their optional elements are assigned to Null if not specified in job inputs.

Input variables are now evaluated and added to the dependency graph, even when they are optional and not used. They need to be a part of the graph in case they are assigned to other (unused) variables for a proper expression evaluation.

Releases: dnanexus/wdlTools