Errors

By default, whenever SPRAS runs into a container error (i.e. an internal algorithm error), the full workflow will fail. However, there are certain designated errors where we don’t want this to be the case.

Due to the following design constraints:

• Snakemake does not have support for such errors (the closest being --keep-going, which unnecessarily runs failed runs)

• SPRAS occasionally outputs empty files as genuine output

• We need to log errors that happen for user knowledge

we opt to use an artifact-info.json file, which keeps track of the success/failure status at certain failable parts of the workflow. This file contains whether or not this part of the workflow succeeded, and if it failed, how it failed.

The artifact-info.json stores a JSON object, containing:

• The key status, which is either the value success or error, depending on what happened in the workflow.

• If status is error, we store associated error details in the details key, which contains an object:

  • The details object varies per error in the form of a tagged union: they are differentiated by the type key. We describe each error down below.

Error Types

With the above schema, we detail the details key below.

Timeout

Timeout has type: "timeout", with a single key duration, which describes the timeout value associated to that run.