OverviewTeaching: 10 min
Exercises: 0 minQuestions
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 InterProScan tool for simultaneously searching protein sequences against a wide variety of resources. It is a good example of a number of good practices in CWL.
cwlVersion: v1.0 class: CommandLineTool label: "InterProScan: protein sequence classifier" doc: | Version 5.21-60 can be downloaded here: https://github.com/ebi-pf-team/interproscan/wiki/HowToDownload Documentation on how to run InterProScan 5 can be found here: https://github.com/ebi-pf-team/interproscan/wiki/HowToRun requirements: ResourceRequirement: ramMin: 10240 coresMin: 3 SchemaDefRequirement: types: - $import: InterProScan-apps.yml hints: SoftwareRequirement: packages: interproscan: specs: [ "https://identifiers.org/rrid/RRID:SCR_005829" ] version: [ "5.21-60" ] inputs: proteinFile: type: File inputBinding: prefix: --input applications: type: InterProScan-apps.yml#apps? inputBinding: itemSeparator: ',' prefix: --applications baseCommand: interproscan.sh arguments: - valueFrom: $(inputs.proteinFile.nameroot).i5_annotations prefix: --outfile - valueFrom: TSV prefix: --formats - --disable-precalc - --goterms - --pathways - valueFrom: $(runtime.tmpdir) prefix: --tempdir outputs: i5Annotations: type: File format: iana:text/tab-separated-values outputBinding: glob: $(inputs.proteinFile.nameroot).i5_annotations $namespaces: iana: https://www.iana.org/assignments/media-types/ s: http://schema.org/ $schemas: - https://schema.org/docs/schema_org_rdfa.html s:license: "https://www.apache.org/licenses/LICENSE-2.0" s:copyrightHolder: "EMBL - European Bioinformatics Institute"
proteinFile: class: File path: test_proteins.fasta
Note: To follow the example below, you need to download the example input file, test_proteins.fasta. The file is available from https://github.com/common-workflow-language/user_guide/raw/gh-pages/_includes/cwl/test_proteins.fasta and can be downloaded e.g. via
On line 34, in
inputs:applications, a list of applications to be used in the
search are imported as a custom object:
inputs: proteinFile: type: File inputBinding: prefix: --input applications: type: InterProScan-apps.yml#apps? inputBinding: itemSeparator: ',' prefix: --applications
The reference to a custom type is a combination of the name of the file in which
the object is defined (
InterProScan-apps.yml) and the name of the object
within that file (
apps) that defines the custom type. The square brackets
mean that an array of the preceding type is expected, in this case the
type from the imported
The contents of the YAML file describing the custom type are given below:
type: enum name: apps symbols: - TIGRFAM - SFLD - SUPERFAMILY - Gene3D - Hamap - Coils - ProSiteProfiles - SMART - CDD - PRINTS - PIRSF - ProSitePatterns - Pfam - ProDom - MobiDBLite
In order for the custom type to be used in the CWL description, it must be
imported. Imports are described in
below in the example
requirements: ResourceRequirement: ramMin: 10240 coresMin: 3 SchemaDefRequirement: types: - $import: InterProScan-apps.yml
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.
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.