Pipeline configuration files
The pipeline configuration file provides all of the information on how to build a pipeline and what tools or pipelines should be used to achieve the desired analysis. This page describes the overall content of one of these pipeline configuration files, but more detail on a number of aspects is provided in companion pages. Finally, a tutorial is provided to help in constructing your own pipeline configuration file.
Following is a list of the fields that can be included in the pipeline configuration file.
Required fields
Each pipeline is given a unique id, which is usually just the name of the pipeline.
configuration type
gkno recognises two types of configuration files; tool and pipeline. The contents of these two files are different and are subject to different checks by gkno and so the type needs to be specified as pipeline for all pipeline configuration files.
A pipeline description must be supplied and should be as descriptive as possible. This description will appear in the pipeline help message, but also on the website help page.