Minor fixes

• Improved support for conditionals and optional values
• Automated tests for both locked and regular workflows
• Various minor bug fixes

Regular workflows

• More accurate detection of the IO classes in dx:applets.
• Improved handling of WDL constants. For example, multi word
  constants such as ["1", "2", "4"], and 4 + 11 are recognized as
  such. When possible, they are evaluated at compile time.
• Revert default compilation to a regular workflow. It is possible to
  compile to a locked-down workflow by specifying -locked on the
  command line. To specify command workflow inputs from the command line
  use:

dx run foo -i0.N=19

Minor fixes

Not closing dx:workflows. This turns out to be too restrictive. For example, you cannot add a description to a closed workflow.

Using DNAx workflow inputs and outputs

• Uplift the code to use DNAnexus workflow inputs and outputs.
  Running a workflow now has slighly easier command line syntax.
  For example, if workflow foo takes an integer
  argument N, then running it through the CLI is done like
  this:

dx run foo -iN=19                                                                                                      

• Revamp the conversions between dx:file and wdl:file. This allows
  specifying dx files in defaults.

• Initial support for non-empty WDL array types, for example Array[String]+.

• Improved handling of optional values

• An experimental new syntax for specifying inputs where the workflow
  is underspecified. WDL allows leaving required call inputs unassigned, and
  specifying them from the input file. For example, workflow math
  calls task add, but does not specify argument b. It can then
  be specified from the input file as follows: { "math.add.b" : 3}.

task add {
    Int a
    Int b
    output {
        Int result = a + b
    }
}

workflow math {
    call add { input: a = 3 }                                                                                          
    output {                                                                                                           
       add.result                                                                                                      
    }                                                                                                                  
}

The dx:workflow that is compiled from math can set this variable from
the command line as follows:

dx run math -iadd___b=5                                                                                                

This command line syntax may change in the future.

Minor improvements

• Adding a -quiet flag to suppress warning and informational messages during compilation.
• Minor fixes

Docker images and lazy download

Support docker images that reside on the platform.

Tasks that have an empty command section do not download files eagerly. For example, if a task only looks at size(file), it will not download the file at all.

task fileSize {
    File in_file

    command {}
    output {
        Float num_bytes = size(in_file)
    }
}

Type lookup and evaluation improvements

• Fixed several WDL typing issues
• Removed limitation on maximal hourly price per instance. Some bioinformatics pipelines
  regularly require heavy weight instances.
• Improved the internal representation of JSON objects given as input

Improving scatters

• Handle scatters where the called tasks return file arrays, and non-native platform types. This is done by spawning a subjob to collect all the outputs and bundle them.
• Support string interpolation in workflow expressions
• Support Azure us-west region

0.47

Support calling native dx applets, and adds a tool for automatically creating WDL interfaces for native applets.

Allowing defaults for task/workflow inputs

• Allow applet/workflow inputs that are optional, and have a default.
• More friendly command line interface