Hands-on: Creating workflow runs

• 20 min
• Easy

Once you have imported or created workflow versions, you are ready to associate Workflow Runs to them.

By Workflow Runs, we mean here the execution of a specific Workflow Version on input datasets using specific configuration & parameters, and the resulting output datasets.
Registering workflow runs in LabID allows to easily keep track of the workflow version, and files used, as well as tracking additional metadata about the runs (date of execution, duration...).

Note

We recommend first "releasing" a workflow versions in LabID before associating it to workflow runs !

Example of a nextflow run registered in LabID

Config file used for this run and resulting output datasets

While you can import workflow invocations from a galaxy instance, for other workflow managers you currently have 2 options to register Workflow Runs:
- manually create a workflow run in the web interface
- use the command line interface (CLI) to register workflow runs automatically

Create a workflow run in the web interface

Recording a workflow run in the web interface is rather straightforward.

Step 1 : Create a new workflow run

First go the page with the list of workflow runs, then click at the top left on New Workflow Run and select New workflow run.

Start by clicking the + New workflow run button on the list of workflow run page

Step 2 : Select workflow version and fill-in metadata

Provide information for the 3 required fields:

• a meaningful name for the run,
• which workflow version was used, and
• the status of the run (successfully completed, failed, cancelled...).

You can also edit the visibility of this run to other users, just like any other LabID items. All this fields can be edited at a later time.
Click Save item to finalize the creation of the "blank" workflow run.

Note

You may create a workflow run in LabID before the corresponding execution is terminated.
Just set the status to PENDING or RUNNING then edit this status once you connect the results.
This can be convenient for e.g long-running workflows that you already want to document.

Fill-in the name, workflow version and status for the run

Step 3 : Associate datasets to the run

For each of the dataset tab of the workflow run, you can associate datasets by clicking the Link button at the top of the tab panel.
You can only associate datasets registerd in LabID and visible to you (or your group).
For output datasets, only datasets that you own can be associated (click the Personal at the top right in the list of datasets to filter the list).
You can also unlink previously associated datasets in case of mistake, unlinking does not remove the dataset from the database, it only removes the association of the dataset with this run.

Linking datasets to the run

Exporting workflow runs as RO-Crate

LabID can generate Workflow Run RO-Crate from workflow runs.
Simply click RO-Crate at the top right of the page to download a zip of the workflow run (be patient, this may take some time depending on the number and size of files).
Such file can be used to publish the WorkflowRun to e.g Zenodo or to import it in another RO-Crate-capable software.

Workflow Run RO-Crate can be large !

By default, the WorkflowRun RO-Crate contains all input and output datasets used for the run.
This can represent a large amount of data and result in a fairly large zip file !

Export as RO-Crate available for Workflow versions too

You can also "just" export the workflow version from the workflow version page.
See Exporting workflow versions.