Skip to content Skip to footer

Adding files

The page you are taken to presents four options for registering a workflow and its associated files.

Recommendation

We recommend referencing the files, for example towards a GitHub repo, since we want to be a hub and not a repository for workflows.

This also allows us to show the source link of the RO-Crate on the workflow page and include this in the RO-Crate metadata. In case the referencing would not work, for example with referencing Galaxy instances, you can always use the source metadata field later in the registration.

Upload / import a local file

  1. Select your local workflow file using the Browse… button
  2. Pick your workflow type - if your workflow type is not included in the list you can select Other or add a New workflow type using the available button.
  3. Optional: add in a Abstract CWL using the Browse… button
  4. Optional: add in a Diagram file using the Browse… button
  5. Click the Register button

Select your local file, then select Workflow type. In Abstract CWL either upload from local file or remote URL, same for Diagram. Then click Register.

Fig 2. New workflow tab for uploading / importing local files.

Upload / import using a remote file URL

  1. Add your remote file URL - click Test to check the URL
  2. Pick your workflow type - if your workflow type is not included in the list you can select Other or add a New workflow type using the available button.
  3. Optional: add a remote URL for the Abstract CWL - click Test to check the URL
  4. Optional: add a remote URL for the Diagram file - click Test to check the URL
  5. Click the Register button

Fill in your remote file URL, then select Workflow type. In Abstract CWL set remote URL, same for Diagram. Then click Register.

Fig 3. New workflow tab for importing files from a remote URL.

Importing a Git repository

  1. Add your Git repository URL e.g. https://github.com/username/repository_name
  2. Click the Register button

Add your git URL, then click Register.

Fig 4. New workflow tab for importing files from a git repository (e.g. GitHub, GitLab).

  1. When you have selected to import a specific Git repository URL (i.e. by clicking Register) you will be prompted to specify either a repository:
    • Branch, or
    • Release tag
  2. Once you click Register again, you will gain access to a drop down list of the files in the repository - pick the [main executable workflow file](#bookmark=id.ew79aaxs5ncv):
    • For a NextFlow workflow for example, this would be the .nf file
    • For a series of bash scripts, this would be the first .sh file or the README.md file
  3. You can now pick additional optional files as well:
  4. Click Continue to proceed to the metadata stage

First select branch or a release tag, then use drop down list to select the main executable workflow file. Add any optional files before clicking Continue

Fig 5. Selecting a target branch or release tag as well as the main executable and optional files during Git repository import.

Upload / Import a workflow RO-Crate

  1. Add an RO-Crate zip file, either via:
    1. A local file upload using the Browse… button, or
    2. By adding a remote file URL - click Test to check the URL
  2. Click the Register button

For the zipped RO-Crate, either upload your local file or fill in remote URL, then click Register

Fig 6. New workflow tab for importing files using a Research Object Crate (RO-Crate).