Viash 0.7.4

Minor bug fixes and minor improvements to VDSL3

New Release
Author

Viash Team

Published

May 31, 2023

What’s new?

Some small fixes and consistency improvements. A few Quality of Life improvements were made e.g. to override the Docker entrypoint when working with Nextflow and providing default labels when building a Nextflow workflow.

Full changelog

NEW FUNCTIONALITY

  • Add default labels in Nextflow config files that set default values for cpu and memory settings (PR #412). Values are more or less logarithmically spaced (1, 2, 5, 10, …).

  • Author: Added info field to authors. Deprecated props field (PR #423).

  • viash config view and viash ns list: Set the .info.output path when a platform argument is provided.

  • viash ns exec: Added two more fields:

    • {output}: path to the destination directory when building the component
    • {abs-output}: absolute path to the destination directory when building the component

  • DockerPlatform: Add entrypoint and cmd parameters to the docker platform config that allows overriding the default docker container settings (PR #432).

MINOR CHANGES

  • Nextflow VDSL3:

    • Add profiles to the Nextflow Config file when the main script is a NextflowScript (#408).
    • Add a script parameter in Nextflow Config file to add a single string or list of strings to the nextflow.config (PR #430).

  • Scripts: Remove the entrypoint parameter for all script types except NextflowScript (#409). All these scripts had to check individually whether the parameter was unset, now it can be done in the Script apply method.

  • schema export:

    • Restructure Nextflow-Directives, -Auto and -Config into a nextflowParameters group (PR #412). Previously only NextflowDirectives was exposed.
    • Restructure the format to group authors & computational requirements together with functionality (PR #426).
    • Restructure the Viash Config and Project Config pages under a config category (PR #426).
    • Add references in Functionality and Nextflow VDSL3 to the new documentation pages (PR #426).
    • Add description and/or examples for platforms and requirements (PR #428).

BUG FIXES

  • viash config inject: Fix an empty line being added at the script start for each time viash config inject was run (#377).

  • WorkflowHelper: Fixed an issue where passing a remote file URI (for example http:// or s3://) as param_list caused No such file errors.

  • BashWrapper: Fix escaping of the included script where a line starting with a pipe character with optional leading spaces is stripped of the leading spaces and pipe character. This was quite unlikely to happen except when viash config inject was called on a Nextflow Script, which lead to no real config code being injected however workflows were getting corrupted. (#421)

  • Deprecation testbench: Add missing classes to be checked (PR #426).