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Fixed

  • Bug 274, losing pipe symbols ('|') at the beginning of a line.

Changed

  • Upgrade to Cromwell 44, with support for JSON-like values in meta sections

Added

  • Ability to put a list of upstream projects into the extras file.
Assets 3

@orodeh orodeh released this Jul 4, 2019 · 10 commits to master since this release

Fixed

  • Tolerate platform applets/workflows with input/output specs that use non WDL types. For example, an array of applets.
  • Bug when accessing call results that were not executed. For example, in path_not_taken the compare call is not made. This, incorrectly, causes an exception to be raised while evaluating equality.
version 1.0

workflow path_not_taken {
    if (false) {
        call compare
    }
    output {
        Boolean? equality = compare.equality
    }
}

task compare {
    command {}
    output {
        Boolean equality = true
    }
}

Changed

  • Removed warning for variables that cannot be set from the inputs file. These are messages like this:
Argument unify.contig_shards, is not treated as an input, it cannot be set
Argument etl.shards, is not treated as an input, it cannot be set
Argument seq.iter_compare, is not treated as an input, it cannot be set

Top level call argument can now be set.

Assets 3

@orodeh orodeh released this Jul 3, 2019 · 12 commits to master since this release

Fixed

  • Default values specified for top-level calls using a JSON file.
  • Bug 272
  • Runtime error when using an array of WDL structs

Changed

  • Upgrade to Cromwell v43
  • Replaced internal implementation of finding source lines for calls, with Cromwell/WOM implementation.
Assets 3

@orodeh orodeh released this Jun 26, 2019 · 16 commits to master since this release

Fixed

  • Handling of pair type in a JSON input file
  • Allow overriding default values in calls from the input file. For example, in a workflow like:
version 1.0

workflow override {
    call etl { input: a = 3 }
    output {
        Int result = etl.result
    }
}

task etl {
    input {
        Int a
        Int b = 10
    }
    command {}
    output {
        Int result = a + b
    }
}

We can now set b to a value other than 10, with an input file like this:

{
  "override.etl.b" : 5
}

New

  • Support for compressed docker images (gzip)

Changed

  • Upgrade to Cromwell v42
Assets 3

@orodeh orodeh released this Jun 7, 2019 · 20 commits to master since this release

Fixed

  • The -p flag was not respected
  • Environment not passed correctly during compilation.
  • Sorting structs by dependencies
Assets 3

@orodeh orodeh released this Jun 5, 2019 · 22 commits to master since this release

Fixed

  • bug #259. Unified the code for resolving platform paths.
  • Error when downloading a file that resides in a container, rather than a project.
  • Imports specified from the command line

Changed

  • Merged DxPath and DxBulkResolve modules.
Assets 3

@orodeh orodeh released this Jun 1, 2019 · 27 commits to master since this release

Fixed

Assets 3

@orodeh orodeh released this May 31, 2019 · 28 commits to master since this release

New

  • Upgrade to Cromwell v41
  • Mark auxiliary workflows and applets as hidden. This is a step in the direction of supporting copying of a workflow from one project to another.
  • Use the dx-download-agent (dxda) instead of dx download in tasks. This should make downloads run in parallel, and use bandwidth on large instances better.

Minor

  • Added unit tests for the WomValueAnalysis module, which checks if WOM expressions are constant.
  • Reducing reliance on the dxjava library, calling the DXAPI directly.
  • Merged fork of the dxjava library back into the dx-toolkit.

Bug fixes

  • Fix for bug (#254)
  • Fix for bug occurring when a struct is imported twice
Assets 3

@orodeh orodeh released this May 13, 2019 · 39 commits to master since this release

  1. DxNI working for DNAnexus apps and applet.
  2. Added links to applets that are referenced inside WDL fragments. This is a prerequisite for copying between projects.
  3. Moved applet meta-information into the details field. This makes applets more readable.
  4. Wrote unit-tests for the WdlVarLinks module.
  5. Batching file-describe, and file-resolve calls. Reduces API load, and improves speed, especially when using many files.
Assets 3

@orodeh orodeh released this May 7, 2019 · 43 commits to master since this release

  • Precalculate instance types. There are tasks that calculate the instance type they need in the runtime section. If the task call is made from a workflow fragment, we can calculate the instance type then and there. This allows launching directly in the correct instance type, instead of launching an additional job.
  • Fixed bug in expression evaluation at runtime (#240)
  • Improved unit-test coverage
Assets 3
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