Minor fixes

• Throw an exception if a wrapper for a native platform call has a non-empty runtime section.
• Use an SSD instance for the collect sub-jobs.
• Remove the runtime check for calling a task with missing values, fix issue (#112). The check is overly restrictive. The task could have a default, or, be able to tolerate the missing argument.

Preparation for integration into the dx-toolkit

• Color coding outputs, yellow for warnings, red for errors.
• Indenting information output in verbose mode
• Removing the use of dx pwd. The user needs to specify the
  destination path on the command line. A way to avoid this, is to compile
  from the dx-toolkit, with the upcoming dx compile command.

Minor fixes

• Allow variable and task names to include the sub-string "last"
• Workflow fragment applets inherit access properties from the extras file.

Minor fixes

Ignoring unsupported runtime attributes, as requested in #133.

WDL headers, and setting default values

• Decomposing a workflow when there is a declaration after a call. For example,
  workflow foo needs to be decomposed. The workflow fragment runner does not
  handle dependencies, and cannot wait for the add call to complete.

workflow foo {
    Array[Int] numbers

    scatter (i in numbers) {                                                                                                     
        call add { input: a=i, b=1}                                                                                              
        Int m = add.result + 2                                                                                                   
    }                                                                                                                            
                                                                                                                                 
    output {                                                                                                                     
        Array[Int] ms = m                                                                                                        
    }                                                                                                                            
}

• Setting debug levels at runtime. The compiler flag runtimeDebugLevel can be set to 0, 1, or 2.
  Level 2 is maximum verbosity, level 1 is the default, zero is minimal outputs.

• Upgrade to Cromwell version 32.

• Using headers to speed up the workflow decomposition step. The idea
  is to represent a WDL file with header. When a file is imported, we
  use the header, instead of pulling in the entire WDL code, including
  its own imports.

• Support setting defaults in applets, not just workflows. This can be done with the --defaults
  command line option, and a JSON file of WDL inputs.

Calling apps, and DNAx attributes for tasks

• Support dnanexus configuration options for tasks. Setting
  the execution policy, timeout policies, and access
  control can be achieved by specifying the default option in the
  default_taskdx_attributes section of the extras file. For
  example:

{
  "default_task_dx_attributes" : {
    "runSpec": {
        "executionPolicy": {
          "restartOn": {
            "*": 3
          }
        },
        "timeoutPolicy": {
          "main": {
            "hours": 12
          }
        },
        "access" : {
          "project": "CONTRIBUTE",
          "allProjects": "VIEW",
          "network": [
            "*"
          ],
          "developer": true
        }
      }
  }
}

• Added support for calling native DNAx apps. The command

java -jar dxWDL.jar dxni -apps -o my_apps.wdl

instructs the compiler to search for all the apps you can call, and create WDL
tasks for them.

• Improved error message for namespace validation. Details are no longer hidden when
  the -quiet flag is set.

• Reduced logging verbosity at runtime. Disabled printing of directory structure when running
  tasks, as the directories could be very large.

• Optimization for the case of launching an instance where it is
  calculated at runtime.

Improvements for the atac.wdl pipeline

• Support for setting defaults for all task runtime attributes has been added.
  This is similar to the Cromwell style. The extras command line flag takes a JSON file
  as an argument. For example, if taskAttrs.json is this file:

{
    "default_runtime_attributes" : {
      "docker" : "quay.io/encode-dcc/atac-seq-pipeline:v1"
    }
}

Then adding it to the compilation command line will add the atac-seq docker image to all
tasks by default.

java -jar dxWDL-0.44.jar compile test/files.wdl -defaults test/files_input.json -extras taskAttrs.json

• Reduced the number of auxiliary jobs launched when a task specifies the instance type dynamically.
  A task can do this is by specifiying runtime attributes with expressions.
• Added the value iterated on in scatters

Cromwell-v31, and closed dx workflows

• Upgrade to cromwell-31 WDL/WOM library
• Report multiple validation errors in one step; do not throw an exception for the first one and stop.
• Reuse more of Cromwell's stdlib implementation
• Close generated dx workflows

Bug fix release

Bug fix for case where optional optional types were generated. For example, Int??.

Nested scatters and conditionals

• Nested scatters and if blocks
• Support for missing arguments has been removed, the compiler will generate
  an error in such cases.