Skip to content Skip to footer

Glossary

General

Project also called “Team”
Workflow type See supported workflow types
Organisation
Space
Main workflow file

(mandatory)

 This is the main workflow file that has to be uploaded/referenced.

Specify the Workflow type of the main workflow in the dropdown list:

  • Common Workflow Language(.cwl),
  • Galaxy(.ga),
  • KNIME(.knwf),
  • Nextflow(.nf) or
  • Snakemake(.snake).
  • If your workflow type is not listed, please choose other
Git repository
Remote file URL
CWL abstract
(optional) 		The CWL abstract is used as a summary of the workflow to parse for example the description (doc) if provided or to generate a svg diagram. If you have a Galaxy workflow you can generate the CWL abstract with galaxy2cwl. If your main workflow is a CWL workflow, you can skip this step. In the future it will also be possible to convert other workflow types to CWL abstract.
Diagram
(optional) 		If your main workflow file is CWL or you give a CWL abstract, the diagram is automatically generated by the WorkflowHub website. In any other case you want a diagram in the RO-Crate and on the WorkflowHub website, you will have to supply one yourself. In the upload/reference fields you can attach your diagram in .svg (preferred) or .jpeg/.png.
RO-Crate Research Object Crate: https://www.researchobject.org/ro-crate/

Extra Galaxy information

How to use Galaxy Information on how to use galaxy can be found on the Galaxy Training Network.
Extract a workflow from the History This is the most easy way to generate a Galaxy workflow and is extensively explained here.
Editing a Galaxy workflow Using the Galaxy workflow editor it is recommended to add tags and/or add for example the tutorial title as Annotation/Notes. More information on how to use the editor can be found here in the "The workflow editor" section.
Galaxy to CWL abstract Galaxy workflows can easily be converted to CWL abstract with galaxy2cwl. This can be seen as a standardized summary of the workflow that can be interpreted by WorkflowHub. CWL abstract can also be used to generate a diagram.
Uploading to WorkflowHub Since it is not possible to reference a workflow in a Galaxy instance, you either have to download the workflow file and upload it to WorkflowHub, or make an RO-Crate following the steps below. You can still reference the workflow in the galaxy instance using the source property in the metadata of the registration.

Extra Common Workflow Language (.cwl) information

Home page https://www.commonwl.org/
Community workflows page https://github.com/common-workflow-library

Extra Nextflow (.nf) information

Home page https://www.nextflow.io/
Community workflows page https://nf-co.re/

Extra SnakeMake (.snake) information

Home page https://snakemake.readthedocs.io/en/stable/
Community workflows page https://github.com/snakemake-workflows

Extra KNIME (.knwf) information

Home page https://www.knime.com/
Community workflows page https://hub.knime.com/