Viash 0.5.15

What’s new?

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

Full changelog

BREAKING CHANGES

• WorkflowHelper::helpMessage: Now only takes one argument, namely the config.

MAJOR CHANGES

• Namespace: Changed the namespace of viash from com.dataintuitive.viash to io.viash.

MINOR CHANGES

• Testbenches: Add a testbench framework to test lots of character sequences, single or repeating to be tested in the yaml config. This can be used to later extend to other tests.

• Testbenches::vdsl3: Add testbenches to verify functionality:

  • Vdsl3’s param_list (yamlblob, yaml, json, csv).
  • Nextflow’s own params-file.
  • Vdsl3’s recalculating resource file paths to be relative to the param_list file instead of the workflow file (only available for yaml, json, csv).
  • Vdsl3’s wrapping of modules to run these as a separate workflow automagically out of the box.

• Main: Added viash --schema_export which outputs a schema of the Viash config file to console. This is to be used to automate populating the documentation website.

• Helper: Split help message by argument group.

• Helper: Remove unneeded arguments.

• Functionality: Add default groups Inputs, Outputs and Arguments for all arguments missing from user-defined argument_groups.

• WorkflowHelper::helpMessage: Rewrite to bring on par with Viash’s help message.

• BooleanArguments: Renamed internal class names for BooleanArguments to be better in line with how they are named in the config yaml. BooleanArgumentRegular -> BooleanArgument (in line with boolean) BooleanArgumentTrue -> BooleanTrueArgument (in line with boolean_true) BooleanArgumentFalse -> BooleanFalseArgument (in line with boolean_false)

BUG FIXES

• NextflowVdsl3Platform: Change how --id is processed when a VDSL3 module is called from the CLI.

• NextflowVdsl3Platform: Fix error when param_list is null.

• NextflowVdsl3Platform: Fix error when optional, multiple arguments are set to null.

• Testbenches: Better capture expected error messages while running testbenches again. Code changes right before previous release re-introduced some of the messages.

• NextflowVdsl3Platform: Fix issue where optional parameters aren’t removed when .run(args: [optarg: null]).

• WorkflowHelper::readCsv: Treat empty values as undefined instead of throwing an error.

• NextflowVdsl3Platform: Use $NXF_TEMP or $VIASH_TEMP as temporary directory if the container engine is not set to docker, podman or charlieengine, else set to /tmp.

• Resources: When adding a resource folder, allow a trailing / at the end of the path. Previously this caused the target folder to be erased and the content of the resource folder to be written directly into the target folder.