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