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Schema validation

To perform automatic validation of parameters:

  • Define a schema.yaml detailing the necessary parameters.
  • (Optional) Define any necessary custom types and approriate validation functions
    • The custom schema type must define a custom_schema_types namespace containing a Map types with keys being the type and the values being the function for validating the type.
    • For an example, see custom types
  • In methods.config, include the schema.config file and call the validation functions:
    • (Optional) If a custom schema is defined, call schema.load_custom_types("/path/to/custom/schema.config")
    • Call schema.validate(), optionally with an argument pointing to the schema.yaml file. By default, "${projectDir}/config/schema.yaml" will be used.

Available types

  • Integer
  • String
    • With this type, an additional definition allow_empty can be specified to allow an empty string as input. By default, empty strings will not be allowed.
  • Number
  • List
  • Bool
  • Namespace
    • a Groovy Map
  • Path
    • With this type, an additional definition mode must be specified, indicating whether the associated parameter needs to be readable (mode: 'r') or writeable (mode: 'w')

Available custom types

  • InputNamespace - Validation type for a namespace specifying inputs
input: <<InputNamespace>>
    BAM:
        ...
  • ListFASTQPairs - Validation type for a list of FASTQ pair Maps
input:
    FASTQ: <<ListFASTQPairs>>
        - read_group_identifier: <readgroup ID>
          sample: <sample ID>
          ...
        - read_group_identifier: <readgroup ID>
          sample: <sample ID>
          ...
  • InputBAMNamespace - Validation type for a namespace containing BAMs
input:
    BAM: <<InputBAMNamespace>>
        normal:
            - "/path/to/bam"
            - "/path/to/bam"
        tumor:
            - "/path/to/bam"
            - "/path/to/bam"
  • BAMEntryList - Validation type for a list of BAMs
input:
    BAM:
        normal: <<BAMEntryList>>
            - "/path/to/bam"
            - "/path/to/bam"
        tumor: <<BAMEntryList>>
            - "/path/to/bam"
            - "/path/to/bam"

Available functions

  • validate - The entrypoint function for validating the parameters
    • Positional args:
      position name type required default description
      1 file_path String No "${projectDir}/config/schema.yaml" Path to the schema.yaml file
  • load_custom_types - Function for loading custom types
    • Positional args:
      position name type required default description
      1 custom_types_path String Yes null Path to config file defining custom types
      2 purge_existing_custom_types Boolean No false Option to overwrite previously loaded custom types
  • validate_parameter - Function for recursively validating a parameter
    • Positional args:
      position name type required default description
      1 options Map Yes none Map object where parameter should be defined
      2 name String Yes none Name of the parameter
      3 properties Map Yes none Map object containing the schema properties for the parameter to validate
  • check_path - Function for validating paths and proper permissions
    • Positional args:
      position name type required default description
      1 p String Yes none Path to to validate
      2 mode String Yes none Permission to check, w to check if path is writeable and r to check if path is readable
  • validate_specific - Function for validating specific namespaces and schemas along with an exclusion list
    • Positional args:
      position name type required default description
      1 file_path String or Map Yes none Path to the schema.yaml file or loaded schema as a Map
      2 params_to_validate Map Yes none Namespace of parameters to validate
      3 keys_to_exclude List No [] List of parameters to skip validation

Example

To perform validation, load custom types, if any, and call the validate function.

Example:

includeConfig "/path/to/schema.config"
...
methods {
    ...
    setup = {
        ...
        schema.load_custom_types("/path/to/custom.config")
        schema.validate()
    }
}