Viash 0.4.0

Config mod DSL and renames to viash ns arguments

New Release
Author

Viash Team

Published

April 14, 2021

What’s new?

The viash ns command’s –namespace argument has been renamed to –query_namespace, introduction of custom DSL for overriding config properties at runtime.

Full changelog

NEW FEATURES

  • Config modding: A custom viash DSL allows overriding viash config properties at runtime. See online documentation for more information. Example:

    viash ns test \
  -p docker \
  -c '.functionality.version := "1.0.0"' \
  -c '.platforms[.type == "docker"].target_registry := "my.docker-registry.com"' \
  -c '.platforms[.type == "docker"].setup_strategy := "pull"' \
  -l

  • viash build: The image can be pushed with --push. The same can be done by passing ---push to a viash executable.

  • viash ns can query the name, namespace, or both, with the following arguments:

    • --query_namespace or -n: filter the namespace with a regex.
    • --query_name: filter the name with a regex.
    • --query or -q: filter the namespace/name with a regex.

  • Added the project_build, project_clean, project_push and project_test components to this repository.

  • Added a field .functionality.info of type Map[String, String] in order to be able to specify custom annotations to the component.

BREAKING CHANGES

  • viash ns: Argument --namespace has been renamed to --query_namespace.

  • viash ns: Argument --namespace does not implicitly change the namespace of the functionality anymore. You can use the command DSL to reproduce this effect; for example: -c '.functionality.namespace := "foo"'.

  • Docker & NXF: Attribute version is deprecated. Instead, the default value will be .functionality.version, which can be overridden by using the tag attribute.

  • NXF: When running a viash component as a Nextflow module on its own, you now need to specify all input files on the command line. For instance, if --input and --reference are input file arguments, you need to start the process by running nextflow run main.nf --input <...> --reference <...> <other arguments>. Previously only the input file needed to be specified.

  • Docker & NXF: Default separator between namespace and image name has been changed from "/" to "_".

MINOR CHANGES

  • Docker & NXF: Parsing of image attributes for both Docker and Nextflow platforms are better aligned. You can define an image by specifying either of the following:
    • { image: 'ubuntu:latest' }
    • { image: ubuntu, tag: latest }
  • Docker & NXF: Allow changing the separator between a namespace and the image name.

NEXTFLOW REFACTORING

The generation of Nextflow modules has been refactored thoroughly.

  • NXF: The implicitly generated names for output files/directories have been improved leading to less clashes.

  • NXF: Allow for multiple output files/directories from a module while keeping compatibility for single output. Please refer to the docs.

  • NXF: Allow for zero input files by means of passing an empty list [] in the triplet

  • NXF: Remove requirement for function_type: todir

  • NXF: It is now possible to not only specify label: ... for a nextflow platform but also labels: [ ...].

BUG FIXES

  • Allow quotes in functionality descriptions.

  • NXF: Providing a default: ... value for output file arguments is no longer necessary.