Pipelines

Pipeline Overview

In the most basic sense, a pipeline (or "workflow") is an analysis process which consists of a set of discrete but connected tasks.

Pipelines in Bioinformatics

In the field of bioinformatics, the term "workflow" has taken on the more specialized meaning of a computational analysis which consists of multiple discrete tasks which can be organized into a directed acyclic graph, with the outputs of some tasks providing the inputs to others.

Terminology Note: You may see the various terms 'workflow', 'process', and 'pipeline' used interchangeably. While 'workflow' has taken on the above meaning in bioinformatics, the Cirro platform uses the term 'process' to describe an analysis which can be executed on a dataset, and which invokes a workflow on the back-end. Because the term 'process' is rather generic, the term 'pipeline' will be used frequently in the documentation for ease of understanding.

A handful of software projects have been developed to support this approach to computing, most notably Galaxy, Snakemake, Cromwell, and Nextflow.

With the increased adoption of workflow management software many bioinformaticians have taken on the role of "Workflow Developer", focusing their efforts on the development of reproducible computational analysis workflows which can be executed by many different users across institutions and infrastructures.

Pipelines in Cirro

Cirro was built to support the data analysis needs of researchers for robust, reproducible, and publishable analysis of complex datasets.

Curated no-code analysis pipelines:

• DNA Sequencing
• RNA Sequencing
• Single-Cell Sequencing
• Flow Cytometry
• Image Analysis
• Proteomics
• Statistical Analysis
• Targeted Sequencing
• Quality Control
• Microbial Analysis

Deploying custom Nextflow/WDL pipelines:

• Learn how to Add Your Own Workflows to Cirro

Design principles of workflows for cloud computing:

• Read our philosophy on Developing Reproducible Workflows

If you have any questions about how to best analyze your data in Cirro, please contact our support team.