Viash 0.5.14

What’s new?

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.

Full changelog

NEW FUNCTIONALITY

• Functionality: Allow specifying argument groups. Example:

  functionality:
    ...
    argument_groups:
      - name: First group
        arguments: [foo, bar]
        description: Description

• Addition of the viash_nxf_schema component for converting a Viash config (for a workflow) into a nextflow schema file.

• NextflowVdsl3Platform: Use --param_list to initialise a Nextflow channel with multiple parameter sets. Possible formats are csv, json, yaml, or simply a yaml_blob. A csv should have column names which correspond to the different arguments of this pipeline. A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. A yaml blob can also be passed directly as a parameter. Inside the Nextflow pipeline code, params.param_list can also be used to directly a list of parameter sets. When passing a csv, json or yaml, relative path names are relativized to the location of the parameter file.

  Examples:

  nextflow run "target/foo/bar/main.nf" --param_list '[{"id": "foo", "input": "/path/to/bar"}]'
  nextflow run "target/foo/bar/main.nf" --param_list "params.csv" --reference "/path/to/ref"

MAJOR CHANGES

• NextflowVdsl3Platform: The functionality is now slurped from a json instead of manually taking care of the formatting in Groovy.

• NextflowVdsl3Platform: The --help is auto-generated from the config.

MINOR CHANGES

• NextflowVdsl3Platform: Allow both --publish_dir and --publishDir when auto.publish = true.

• NextflowVdsl3Platform: Allow passing parameters with multiplicity > 1 from Nextflow CLI.

• Main: Added viash --cli_export which outputs the internal cli construction information to console. This is to be used to automate populating the documentation website.

• viash ns: Display success and failure summary statistics, printed to stderr.

• DataObject: .alternatives is now a OneOrMore[String] instead of List[String], meaning you can now specify { type: string, name: "--foo", alternatives: "-f" } instead of { type: string, name: "--foo", alternatives: [ "-f" ] }

• BashWrapper: Added metadata field meta_executable, which is a shorthand notation for meta_executable="$meta_resources_dir/$meta_functionality_name"

INTERNAL CHANGES

• Arguments: Internal naming of functionality.arguments is changed from DataObject to Arguments. Change is also applied to child classes, e.g. StringObject -> StringArgument.

• Script: Allow more control over where injected code ends up.

• Restructure type system to allow type-specific arguments.

BUG FIXES

• DockerPlatform: Change org.opencontainers.image.version annotation to functionality.version when set. Additionally fixed retrieving the git tag possibly returning fatal: No names found, cannot describe anything. or similar.

• viash config inject: Fix config inject when .functionality.inputs or .functionality.outputs is used.

• BashWrapper: Don’t add bc as dependency. Only perform integer/float min/max checks when bc is available, otherwise ignore.

• DockerPlatform: Fix inputs & outputs arguments being present twice.

• viash ns test: Silently skip Nextflow platforms as these don’t support tests and will always fail.

• Testbenches: Better capture expected error messages while running testbenches. Having these show on the console could be confusing.

• NextflowVdsl3Platform: Fix issue when running multiple VDSL3 modules concurrently on the same channel.