Viash 0.3.0

Posted November 24, 2020 by Viash Team ‐ 2 min read

config.vsh.yaml is the new standard format, temporary files are removed when using run and test commands, ...

Full changelog:

BREAKING CHANGES

  • File format functionality.yaml is no longer supported. Use config.vsh.yaml or script.vsh.R/py/... instead.

  • viash run and viash test: By default, temporary files are removed when the execution succeeded, otherwise they are kept. This behaviour can be overridden by specifying --keep true to always keep the temporary files, and --keep false to always remove them.

  • NXF: function_type: todir now returns the output directory on the Channel rather than its contents.

NEW FEATURES

  • Added viash ns test: Run all tests in a particular namespace. For each test, the exit code and duration is reported. Results can be written to a tsv file.
  • Added support for JavaScript scripts.
  • Added support for Scala scripts.
  • [NXF] publishing has a few more options:
    • publish: Publish or yes (default is false)
    • per_id: Publish results in directories containing the unique (sample) ID (default is true)
    • path: A prefix path for the results to be published (default is empty)
  • Functionality resources and tests: Allow copying whole directories instead of only single files. Also allow to rename the destination folder by specifying a value for 'dest'.
  • Platform R / Python dependencies: Allow running a simple command.

MAJOR CHANGES

  • The -P <platform> parameter will be deprecated. For now, all -P values are simply passed to -p.
  • viash ns build and viash ns test: Now use all available platforms if -p is not specified.
  • By default, python packages will not be installed as user. Use user: true to modify this behaviour.

MINOR CHANGES

  • Name of autogenerated Docker image is now ns/tool.
  • Internal changes to make it easier to extend viash with more scripting languages.
  • NXF: Default image is now ns/tool for consistency.
  • NXF: Repurpose asis function type for having simple publishing steps (see docs).
  • NXF: Add component name to main process name
  • R dependencies: by default, do not reinstall Bioconductor packages. Set bioc_force_install: true to revert this behaviour.

BUG FIXES

  • viash build: Do not display error messages when pwd is not a git repository.

TESTING

  • viash test: Add tests for viash test functionality.