Overview
Astrocyte is an interface that aims to simplify the sharing and usage of complex workflows for computational research scientists. Astrocyte can be used to analyze large datasets.
As such, it uses a few basic but fairly universal concepts and roles in order to simplify the language.
When possible, Astrocyte terms will be specified with leading caps (e.g. “Run” instead of “run”) or, in a technical context, in code-type (e.g. “run” instead of “run”)
Roles
User: The User is who the Astrocyte workflow is created for - they are the graduate student, new bioinformatician, or colleague who will be running the workflow on their data.
Workflow Developer: The Workflow Developer (often just “the Developer”) is the creator or maintainer of a workflow - they are the expert who has created the workflow, or has translated an existing pipeline to work on Astrocyte.
Components
Workflow: A Workflow (also sometimes referred to as a “pipeline”) is a series of processes which ingest some form of input data and parameters in order to produce a computational result.
- In Astrocyte, Workflows are written using Nextflow as their top-level language, but Nextflow’s flexibility allows a large number of languages to be used to process the input data.
- All workflows available on Astrocyte can be found using the “Browse Workflows” button above.
- Workflows are retained and versioned and are indexed against matching git repositories, so that you can investigate the source code of any pipeline.
- Some workflows come with visualization apps (VizApps) which may be used to further analyze and visualize the outputs of a given Run.
Run: A Run is a single instance of a workflow’s execution, paired with some input data and some input parameters. Currently, each Run is executed on BioHPC using Nextflow, but there are plans to extend this functionality to execute on other platforms using other workflow languages.
- Each Run is managed in a Project (see below). When a Run executes, the working folder (refer to Nextflow documentation) is available for export, either in “output” form, which provides the “intended” output files as defined by the workflow developer, or in “debug” form, which contains all input data, parameters, and commands. As such, debug exports are important to provide to workflow maintainers when troubleshooting.
Project: A Project is an organized set of input data, as well as various Runs which have been executed on that data using a variety of different workflows and different parameters.
- Most workflows require that you have appropriate input data in your Project before they will run correctly.
- Projects can be shared with other Astrocyte users to facilitate collaboration.
Package: An Astrocyte Package is the entire collection of a Nextflow workflow and the necessary Astrocyte package files to describe the web interface, vizapp, documentation, etc. It may also include test data, container images, and supporting libraries.