Pipelines Configuration: Parameter options overrides

[ericenns]

Problem

As an administrator of IRIDA Next I would like to be able to provide my own sets of options for pipeline parameters when I register a pipeline in the system. Specifically I would like to be able to provide a set of database options which would render a select dropdown for a specified database option with a name (visible to the user) and a path which is passed to the pipeline. This would ensure that my Users would be able to launch a pipeline with a given database without having knowledge of our database store. These parameter overrides could be set for a specific version of a pipeline or for any version of the same pipeline.

Summary

• Update pipeline json config at config/pipelines/pipelines.json to support overriding parameters in version config or in pipeline entry.

  [
    {
      "url": "https://github.com/phac-nml/iridanextexample",
      "name": "phac-nml/iridanextexample",
      "description": "IRIDA Next Example Pipeline",
      "parameter_overrides": {
         "database": {
           "description": { # can be left for later
             "en": "Englush fdescpt",
             "fr": "Francais safd"
           },
           "default": "DBNAME",
           "enum": [
            {"DBNAME": "PATH_TO_DB"}
           ]
         }
      },
      "versions": [
        {
          "name": "1.0.2",
          "parameter_overrides": {
            "database": {
              "default": "DBNAME",
              "enum": [
                {"DBNAME": "PATH_TO_DB"}
              ]
            }
          },
        },
      ],
    },
  ]

• Update lib/irida/pipelines.rb to parse the section for the pipeline in register_pipelines to parse parameter_overrides and merge global if present with version specific parameter_overrides
• Update lib/irida/pipeline.rb to include parameter_overrides attr and method to access it
• Update NextflowComponent to check parameter_overrides and if present modify parameter for display