Capsules

Adding a capsule to a pipeline

To add a capsule to the pipeline, drag the capsule from the Add Capsule menu and drop it into the pipeline building area.

If the capsule is not ready to be used in a pipeline a hazard symbol appears beside it. An up-to-date reproducible run is required before a capsule can be used in a pipeline, and all changes must be committed in the capsule for those changes to be reflected in the pipeline. More information on committing changes in a capsule can be found in Version Control.

Using Released Capsules in a Pipeline

Once the capsule is ready to be used in a pipeline, it is best practice to release the capsule. This allows the released version to be used in the pipeline which ensures any subsequent changes to the capsule do not affect the pipeline. See how to release a capsule.

In Add Capsules, capsules with a released version are indicated by the released icon .

When a capsule is dragged and dropped with a released version into the pipeline building area, you can select which version to use.

The version can be changed at any time in the capsule's settings.

Resume A Pipeline Run from any Intermediate Step

A pipeline can be resumed by clicking the Resume Run option in the dropdown menu of a completed run.

The run will automatically resume from the first step in the pipeline at which a change has been made. In this example, the Map Paths menu between FastQC and MultiQC has been changed. The inputs and outputs of FastQC have not changed so by resuming the run the pipeline will start at the MultiQC capsule using the cached output of FastQC. The image below shows the timeline report of the resumed run.

The version used by the pipeline will remain unchanged if a new version of the capsule is released.

Removing a Capsule from a Pipeline

Hover over the capsule and click the garbage can to remove it from the pipeline.