Workflows

SeqCMD leverages Nextflow as its workflow engine.

Workflow Catalog

To run a Workflow using SeqCMD it must be registered in the workflow catalog. A Workflow is a pointer to a git repository containing the scripts and configuration necessary to run the Workflow on AWS Batch. To register a new Workflow you will specify the location of the Git repository, the version, where the output should be published to. To enable workflows to be iteratively improved SeqCMD allows multiple versions of a workflow to be registered. For each workflow there is a single "Default" version of the workflow. This marker is provided to help users identify the current version of a workflow, and is selected by SeqCMD when workflows are triggered without user input (by event-driven automation).

Queue

Executions of a particular workflow, including the exact version of the workflow and parameters used to run the workflow, are indexed in the "Queue" tab of the main navigation bar. Links on the execution records can be used to navigate to the AWS Batch to retrieve low-level execution details. Workflows can optionally generate a "report.html" output to provide a high level summary of their execution to the user.