Custom Types

Overview

Teaching: 10 min
Exercises: 0 min
Questions
  • How do I create and import my own custom types into a CWL description?

Objectives
  • Learn how to write custom CWL object types.

  • Learn how to import these custom objects into a tool description.

Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly.

The example below is a CWL description of the biom convert format tool for converting a standard biom table file to hd5 format.

custom-types.cwl

#!/usr/bin/env cwl-runner 
cwlVersion: v1.0
class: CommandLineTool

requirements:
  InlineJavascriptRequirement: {}
  ResourceRequirement:
    coresMax: 1
    ramMin: 100  # just a default, could be lowered
  SchemaDefRequirement:
    types:
      - $import: biom-convert-table.yaml

hints:
  DockerRequirement:
    dockerPull: 'quay.io/biocontainers/biom-format:2.1.6--py27_0'
  SoftwareRequirement:
    packages:
      biom-format:
        specs: [ "https://doi.org/10.1186/2047-217X-1-7" ]
        version: [ "2.1.6" ]

inputs:
  biom:
    type: File
    format: edam:format_3746  # BIOM
    inputBinding:
      prefix: --input-fp
  table_type:
    type: biom-convert-table.yaml#table_type
    inputBinding:
      prefix: --table-type

  header_key:
    type: string?
    doc: |
      The observation metadata to include from the input BIOM table file when
      creating a tsv table file. By default no observation metadata will be
      included.
    inputBinding:
      prefix: --header-key

baseCommand: [ biom, convert ]

arguments:
  - valueFrom: $(inputs.biom.nameroot).hdf5  
    prefix: --output-fp
  - --to-hdf5

outputs:
  result:
    type: File
    outputBinding: { glob: "$(inputs.biom.nameroot)*" }

$namespaces:
  edam: http://edamontology.org/
  s: http://schema.org/

$schemas:
  - http://edamontology.org/EDAM_1.16.owl
  - https://schema.org/docs/schema_org_rdfa.html

s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute"

custom-types.yml

biom:
    class: File
    format: http://edamontology.org/format_3746
    path: rich_sparse_otu_table.biom
table_type: OTU table

Note: To follow the example below, you need to download the example input file, rich_sparse_otu_table.biom. The file is available from https://github.com/common-workflow-language/user_guide/raw/gh-pages/_includes/cwl/rich_sparse_otu_table.biom and can be downloaded e.g. via wget:

wget https://github.com/common-workflow-language/user_guide/raw/gh-pages/_includes/cwl/rich_sparse_otu_table.biom

On line 34, in inputs:table_type, a list of allowable table options to be used in the table conversion are imported as a custom object:

inputs:
  biom:
    type: File
    format: edam:format_3746  # BIOM
    inputBinding:
      prefix: --input-fp
  table_type:
    type: biom-convert-table.yaml#table_type
    inputBinding:
      prefix: --table-type

The reference to a custom type is a combination of the name of the file in which the object is defined (biom-convert-table.yaml) and the name of the object within that file (table_type) that defines the custom type. In this case the symbols array from the imported biom-convert-table.yaml file define the allowable table options. For example, in custom-types.yml, we pass OTU table as an input that tells the tool to create an OTU table in hd5 format.

The contents of the YAML file describing the custom type are given below:

type: enum
name: table_type
label: The type of the table to produce
symbols:
  - OTU table
  - Pathway table
  - Function table
  - Ortholog table
  - Gene table
  - Metabolite table
  - Taxon table
  - Table

In order for the custom type to be used in the CWL description, it must be imported. Imports are described in requirements:SchemaDefRequirement, as below in the example custom-types.cwl description:

requirements:
  InlineJavascriptRequirement: {}
  ResourceRequirement:
    coresMax: 1
    ramMin: 100
  SchemaDefRequirement:
    types:
      - $import: biom-convert-table.yaml

Note also that the author of this CWL description has also included ResourceRequirements, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide.

Key Points

  • You can create your own custom types to load into descriptions.

  • These custom types allow the user to configure the behaviour of a tool without tinkering directly with the tool description.

  • Custom types are described in separate YAML files and imported as needed.