0.18

• The deprecated parse, validate, inputs and highlight functionality from the command line tool has been removed in favor of wdltool (https://github.com/broadinstitute/wdltool)
• Workflow options can now include a defaultRuntimeOptions section, so that the same runtime attribute is not needed in every single WDL task. E.g.:

{
  "defaultRuntimeOptions": {
    "docker": "ubuntu:latest"
  }
}

• Changed the JES runtime attributes defaultDisks and defaultZones to be simply disks and zones respectively.
• Liquibase scripts now run automatically. Non-persistent, in-memory databases are not affected. However Cromwell will
  not start if it detects evidence of manually run liquibase migrations in a persistent database. Instead, before Cromwell
  will start cleanly, the database should backed up, and then this SQL should be manually executed:

update DATABASECHANGELOG
  set MD5SUM = null,
    FILENAME = substr(FILENAME, instr(FILENAME, "src/main/migrations/") + length("src/main/migrations/"))
  where FILENAME like '%src/main/migrations/%'

• Added Preemptible VMs support for JES. This has impacts on the API Endpoint responses as a Call/Shard can now be attempted multiple times. Each attempt will have its own entry.
• Added custom thread pool to workaround Slick deadlocks. The thread pool
  size defaults to the Slick configuration value db.numThreads, but may be increased up to Slick's
  db.maxConnections, via a new property actionThreadPoolSize.
• Added support for size WDL standard library function.
• Allow for runtime attribute values to be interpreted as full expressions. For example:

task example {
  String ubuntu_tag
  command { ... }
  runtime {
    docker: "ubuntu:" + ubuntu_tag
  }
}

• Add runtime attributes in Call metadata :

{
  "workflowName": "hello",
  "calls": {
    "hello.hello": [
      {
        ...,
        "runtimeAttributes": {
                  "preemptible": "0",
                  "failOnStderr": "false",
                  "disks": "local-disk 10 SSD",
                  "continueOnReturnCode": "0",
                  "docker": "ubuntu:latest",
                  "cpu": "1",
                  "zones": "us-central1-a",
                  "memory": "2GB"
                },
        ...
      }
    ]
  }
}

• Added "preemptible" field in Call metadata. This only appears if the backend is JES.

{
  "workflowName": "hello",
  "calls": {
    "hello.hello": [
      {
        ...,
        "preemptible": "true"
        ...
      }
    ]
  }
}

0.17

• Validate RuntimeAttributes before starting a call
• Prevent infinite retries
• Persist disallowed return codes in DB
• Add deprecation notices to WDL specific command line functionality
• Make Call backoff polling backend specific
• Aborts jobs on shutdown.
• Numerous bug fixes and stability improvements

0.16

• Bug fix: call caching will not calculate MD5s if turned off
• New API endpoint for generating HTML timing diagrams of a workflow
• Move the Scala bindings for WDL into a new project wdl4s

0.15

• Call caching allows Cromwell to use results from prior invocations if it detected that it's run a call in the past
• Various bug fixes, stability improvements
• Improved REST API

0.14

• Improved logging
• Improved concurrency handing for high workflow loads
• Bug fixes
• Improved stability

0.13

• Stability and bug fixes

• implemented read_float(), read_boolean(), read_object(), and write_object() WDL functions

• Allow WDL functions at the workflow level:

  workflow wf {
    Array[Int] my_ints = read_lines("some_file")
  }
  

0.12

Merge branch 'develop'

0.10

• Sun GridEngine backend. Specifying -Dbackend.backend=sge will use qsub to launch jobs. See also the filesystem assumptions for using the GridEngine backend.

• Support for scatter blocks, for example:

  task add_one {
    Int n
    command {
      python -c "print(${n}+1)"
    }
    output {
      Int incremented = read_int(stdout())
    }
  }
  
  workflow test {
    Array[Int] list = [1,2,3,4]
    scatter (x in list) {
      call add_one {input: n=x}
    }
  }
  

• Localization strategies for SGE/local backends. Instead of copying all files, one can specify hard-link, soft-link, and copy. By default they are tried in the order that they're listed here until one succeeds, though the priority is configurable. See filesystem assumptions for more information.

0.9

• Updated parser for the new specification changes
• Fix bugs in JES backend

0.8

• API Endpoints for validating
• Stability / bug fixes
• Newline characters are now not stripped from the command section