Viash Blog – Viash

Viash 0.8.8

Hotfix for Nextflow edge

This is a hotfix release for the changes in Nextflow edge’s handling of double arguments.

Viash 0.9.4

Hotfix for Nextflow edge

This is a hotfix release for the changes in Nextflow edge’s handling of double arguments.

Viash 0.8.7

Backport support upcoming version of Nextflow

The upcoming release of Nextflow introduces a new class for loading scripts and renamed the old class. This release supports this change by using reflection to detect the…

Viash 0.9.3

Support upcoming version of Nextflow

The upcoming release of Nextflow introduces a new class for loading scripts and renamed the old class. This release supports this change by using reflection to detect the…

Viash 0.9.2

Bug fix release

This release fixes an edge case where output arguments for subworkflows were malformed.

Viash 0.9.1

Enhanced nextflow support and Scala 3 update

Workflows can now publish results asynchronously by emitting multiple output channels. These results will then be merged into a published output behind the screens.…

Viash 0.9.0

Restructure platforms into runners and engines

This release restructures the introduces changes to the Viash config: - The platforms field is split into runners and engines - The .functionality layer has been removed…

Viash 0.8.6

Bug fixes and improvements for CI

Fix some issues in some edge cases. Add options for testing in a CI environment. Given that these options are not meant for general use, they are hidden from the help…

Viash 0.8.5

Bug fixes and documentation improvements

Fix a bug when building a test docker container which requires a test resource. Additional improvements for the website documentation and support for the latest version of…

Viash 0.8.4

Fix building components with dependencies that have symlinks in their paths.

Viash 0.8.3

Fix some edge cases and improve usability.

Viash 0.8.2

Minor changes and bug fixes

This release fixes a few bugs regarding dependencies and how the Nextflow platform handles Paths.

Viash 0.8.1

Minor bug fix to Nextflow workflows

This release fixes a bug in the Nextflow platform where calling a workflow with the .run() function without specifying the fromState argument would result in an error when…

Viash 0.8.0

Nextflow workflows and dependencies

Nextflow workflows definitions are picked up by Viash and assembled into a functional Nextflow workflow, reducing the amount of boilerplate code needed to be written by the…

Viash 0.7.5

Minor breaking changes and new features

This release contains minor breaking change due to deprecated or outdated functionality being removed.

Viash 0.7.4

Minor bug fixes and minor improvements to VDSL3

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…

Viash 0.7.3

Minor bug fixes in documentation and config view

Fix minor issues in the documentation and with the way parent paths of resources are printed a config view.

Viash 0.7.2

Project-relative paths and improved metadata handling

This update adds functionality to resolve paths starting with a slash as relative to the project directory, improves handling of info metadata in the config, and fixes to…

Viash 0.7.1

Minor improvements to VDSL3 and schema functionality.

This is a minor release which improves caching in VDSL3 components and changes the formats of the schema files for the Viash config and CLI.

Viash 0.7.0

Major code cleanup and minor improvements to VDSL3

Default namespace separator has been changed from _ to /. This means Docker images will be named <Registry>/<Organization>/<Namespace>/<Name> by default. For example, ghcr.io…

Viash 0.6.7

A minor release with several QoL improvements

Another minor release which contains several quality of life improvements for the Nextflow VDSL3 platform, as well as automated warnings for deprecated functionality.

Viash 0.6.6

A small bugfix release

This release fixes an issue where stderr was being redirected to stdout.

Viash 0.6.5

A small bugfix release

A small update which fixes an issue with viash ns list that was introduced in Viash 0.6.3.

Viash 0.6.4

Add backwards compability by supporting switching to older Viash versions

This release adds features related to managing Viash projects and allows for better runtime introspection of Nextflow VDSL3 modules.

Viash 0.6.3

Quality-of-life improvements in Viash.

This release features contains mostly quality of life improvements and some experimental functionality. Most notably:

Viash 0.6.2

This is a quick release to push two bug fixes related to security and being able to run Nextflow with optional output files.

Viash 0.6.1

Minor improvements in functionality

This release contains mostly minor improvements of functionality released in Viash 0.6.0. Most notably:

Viash 0.6.0

Nextflow VDSL3 is now the default, support for tracking memory and cpu requirements more elegantly

The first (major) release this year! The biggest changes are:

Viash 0.5.15

Added testbenches, default argument groups and bugfixes for VDSL3

This release introduces testbenches and new default argument groups: Inputs, Outputs and Arguments.

Viash 0.5.14

Argument groups can now be defined in the Viash config

Argument groups allow for grouping arguments together by function or category, making the --help output a lot more clear for components with a lot of arguments.

Viash 0.5.13

Added overriding of the container registry for the VDSL3 + VDSL3 bug fixes

VDSL3 gets even more improvements and bug fixes.

Viash 0.5.12

Improvements for VDSL3 and the Bash wrapper + several bug fixes

This release contains a bunch improvements for VDSL3 and adds some parameters to the viash test and viash test ns commands.

Viash 0.5.11

Nextflow VDSL3 is here!

This release contains additional sugar syntax for specifying inputs and outputs in a Viash config, a beta implementation for the next-generation Viash platform, and several…

Viash 0.5.10.1

A quick bug fix

This quick release fixes a bug that prevented the correct passthrough of the new organization field.

Viash 0.5.10

Rework of the Viash helper components

The viash_install, viash_build, viash_test and viash_push components have been reworked.

Viash 0.5.9

Allow interrupting Viash components

The biggest change in this release is that long running Viash components (VS Code server or R Studio server for example) can now be interrupted by pressing CTRL-C or by…

Viash 0.5.8

Allow defining a Docker image organization, and single values can be used in place of lists

DockerPlatform: Allow defining a container’s organisation. Example:

Viash 0.5.7

Argument examples need to be of the same type as the argument itself

Examples for arguments now need to be of the same type as the argument itself. You can’t provide an integer for a string-based argument for example.
A handy new command has…

Viash 0.5.6

Forbidden Bash flags have been renamed

Set version of helper scripts to the same version as Viash.

Viash 0.5.5

Resources dir no longer added to PATH automatically and minor changes

The resources directory is no longer added to the PATH variable by default. You can re-enable this behaviour by setting add_resources_to_path to true in the functionality…

Viash 0.5.4

Added cache directive to specify the typing of caching to be performed for the Nextflow platform

A cache type can now be specified in the config file for the Nextflow platform. Previously this was hardcoded to be deep, but the default caching method is now default.
To…

Viash 0.5.3

New meta data list for scripts, VIASH_TEMP environment variable for Nextflow, fixed output formatting with separate outputs

This release provides more information to scripts with the new meta list. This list contains two values for now:

Viash 0.5.0

Improvements to running Docker executables, and Nextflow platform argument changes

Here are the most important changes:

Viash 0.5.2

More settings for Docker and Nextflow platform, and a bug fixes for components with resources

This is a small release containing two small features and a bug fix. The new run_args field allows you to add docker run arguments to the Docker platform section of a config…

Viash 0.5.1

Viash 0.5.1 adds support for C# scripts and fixes a few bugs

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…

Viash 0.4.0.1

Three small bug fixes.

NXF: Return original_params instead of updated params for now.

Viash 0.4.0

Config mod DSL and renames to viash ns arguments

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

Viash 0.3.2

Don’t auto-generate viash.yaml and add beta unit testing in Nextflow

The viash build command doesn’t generate a viash.yaml automatically anymore, added beta functionality for running tests in Nextflow.

Viash 0.3.1

Add fields for specifying authors and the Docker registry

Add authors field to config, added registry fields to Docker platform config.

Viash 0.3.0

Combine functionality and platform into one config, remove temporary files

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

Viash 0.2.2

Generation of placeholder code now possible without VIASH START and VIASH END

Allow generating placeholder without VIASH START/VIASH END blocks.

Viash 0.2.1

Docker chown by default

Running a script using a Docker platform will now chown output files by default, as well as any temporary files. You can turn off this feature by specifying chown: false in…

Viash 0.2.0

Autoresolve docker paths

Arguments of type: file are processed to automatically create a mount in docker. More specifically, when you pass an argument value: --input /path/to/file, this will be…

Viash 0.1.0

Changes to functionality and the native/docker platforms

ftype has been renamed to function_type. The value for this field is also being checked.
platform has been removed.
Instead, the first resource listed is expected to…

Say hello to Viash 👋

Introducing Viash, helping you turn a script into a reusable and reproducible Nextflow module to use in your pipelines.

Look out for more info soon!

Viash 0.0.1

Initial release

Initial proof of concept.