Viash 0.5.1

What’s new?

C# script support

We’ve added C# scripts (.csx) as a supported language using dotnet-script.
To run C# scripts natively, you’ll need to install .NET Core and execute the following command in a terminal:

dotnet tool install -g dotnet-script

You can now run C# scripts like this:

dotnet script hello_viash.csx

To use C# scripts as components, use the new csharp_script type in the functionality section of your config file:

  resources:
  - type: csharp_script
    path: script.csx

Here’s an example of a simple C# script with Viash in mind:

// VIASH START
var par = new {
  input = "Hello World",
  name = "Mike"
};
// VIASH END

System.Console.WriteLine(input + ", " + name + "!");

The language-specific guide for creating C# script components will be added in the near future.

Bug fixes

First off, these special characters can now be used in the description, usage, default and example fields of components:

• ”
• `
• \
• $

Nextflow output files with the same extension won’t overwrite each other any more, like it was the case for arguments like this:

functionality:
  name: bar
  arguments:
    - name: "--input"
      type: file
      example: input.txt
    - name: "--output1"
      type: file
      direction: output
      required: true
      example: output.txt
    - name: "--output2"
      type: file
      direction: output
      required: true
      example: optional.txt

In this case, the two output files would have been identical in the past. ___

Full changelog

NEW FEATURES

• CSharpScript: Added support for C# scripts (type: "csharp_script") to viash.

MINOR CHANGES

• NextflowPlatform: Added directive_cpus, directive_max_forks, directive_memory and directive_time parameters.

BUG FIXES

• BashWrapper: Refactor escaping descriptions, usages, defaults, and examples (#34).

• NextflowPlatform: Refactor escaping descriptions, usages, defaults and examples (#75).

• NextflowPlatform: Add argument to output path to avoid naming conflicts for components with multiple output files (#76).

• NextflowPlatform, renderCLI(): Only add flag to rendered command when boolean_true is actually true (#78).

• DockerPlatform: Only chown when output file exists.

TESTING

• viash build: Capture stdout messages when errors are expected, so that they don’t clutter the expected output.

• viash build: Check --help description output on the whole text instead of per letter or word basis.

• TestingAllComponentsSuite: Only testing bash natively, because other dependencies might not be available.