Viash 0.5.11

Nextflow VDSL3 is here!

New Release
Author

Viash Team

Published

May 9, 2022

What’s new?

This release contains additional sugar syntax for specifying inputs and outputs in a Viash config, a beta implementation for the next-generation Viash platform, and several other minor improvements.

Full changelog

MAJOR CHANGES

  • Functionality: Now also accepts ‘inputs’ and ‘outputs’ in addition to ‘arguments’. For inputs and outputs, any specified arguments will have default type: file and direction: input or direction: output respectively.

MINOR CHANGES

  • DockerPlatform: Move description labels to the end of the Dockerfile to improve cross-component caching.

  • Functionality: Arguments where .multiple is true can now have lists as default and example.

  • viash_build: Added unit test for this component.

  • viash_test: Added unit test for this component.

  • PythonRequirements: Allow upgrading dependencies. Example: [ type: python. pypi: anndata, upgrade: true ].

  • NextflowLegacyPlatform: Remove annoying messages when building Nxf modules.

  • ConfigMods: Expanded the DSL to allow specifying at which point to apply a config mod. This functionality was necessary to allow for setting fields which alter the way configs are parsed. Example of when this is useful: <preparse> .platforms[.type == "nextflow"].variant := "vdsl3". Updating workflow of parsing a config file is:

    • read Yaml from file
    • apply preparse config mods
    • parse resulting Json as Config, thereby instantiating default values etc.
    • convert Config back to Json
    • apply postparse config mods (original config mods)
    • convert final Json back to Config

BETA FUNCTIONALITY

  • NextflowVdsl3Platform: A beta implementation of the next-generation Viash+Nextflow platform. See https://github.com/viash-io/viash/issues/82 for more information. You can access the previous Nextflow platform by using the variant parameter:

    - type: nextflow
  variant: legacy
  separate_multiple_outputs: false

BUG FIXES

  • viash_build and viash_test: The query_name and query_namespace arguments were switched around. These arguments are now passed correctly.

  • BashScript, JavaScriptScript, PythonScript, RScript: Correctly escape ' (#113). Update unit tests accordingly.

  • CSharpScript, ScalaScript: Correctly escape " (#113). Update unit tests accordingly.

  • viash_build, viash_test, viash_push: Don’t try to remove log files if they don’t exist.

INTERNAL CHANGES

  • DataObject:
    • Renamed otype to flags.
    • Renamed oType to type
    • Deprecated tag (unused feature).
  • All abstract / inherited classes: Renamed oType to type.

DEPRECATION

  • Functionality: Deprecated function_type and add_resources_to_path. These should be unused features, by now.