Release viash 0.3.0 (2020-11-24) · viash-io/viash

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.

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.

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.

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.