In the INNUENDO Platform, protocols are the basic unit for running processes. They are the building blocks to construct Workflows, which can then be applied to strains in our projects.
Protocol creation is responsibility of the INNUENDO platform administrators.
Protocols are composed of a Type, the name of the used Software, a Nextflow Tag, Parameters, and a Name. Each protocol name MUST be unique.
Protocol types are defined by NGSOnto and are a way of classifying the available protocols. Each type can have different attributes.
- de-novo assembly protocol
- Sequencing quality control protocol
- Allele Call Protocol
- sequencing Protocol
- DNA Extraction protocol
- Pathotyping Protocol
- Sequence cutting protocol
- mapping assembly protocol
- Filtering protocol
- Library Preparation Protocol
When creating a protocol, other field that needs to exist is the used Software. It is required for the Platform to know which software you are going to use on that protocol in case some extra steps are required after or before running it. The available tags are:
- fastqc (fastqc_trimmomatic)
- fastqc_2 (fastqc)
- integrity_coverage_2 (check_coverage)
Each of these tags are closely related to the Nextflow Tags chosen. So, to have a good agreement between Software and Nextflow Tags, pair them together.
The protocol name is the identifier that will appear when choosing protocols to apply to a Workflow. Each protocol name MUST be unique. Also, try to make a reference for the nextflow tag used in the protocol name in order to establish a better organization regarding available protocols.
For more information regarding FlowCraft, checkout this link: https://assemblerflow.readthedocs.io/en/dev/index.html