Set Workflows

In the INNUENDO Platform, Workflows are the merge of one or more protocols to build a cascade of events to be applied to you strains. Their goal is to organize a group of software to be applied and you can then apply multiple workflows to a strain and build a pipeline according to their specific Workflow dependencies.

As for Protocols, Workflows also have a predefined set of attributes that need to be filled in order to be successfully applied to a strain. A workflow must have a Name, a Dependency, a Type, and the Species where that workflow will be available.

Workflows are Species dependent so you need to define the workflows that you want to make available for each species.

Workflow creation is responsibility of the INNUENDO platform administrators.

Workflow Name

Each workflow MUST have a name and it cannot be the same even across Species. The use of special characters are discouraged.

Workflow Dependency

Workflows can have input dependencies that are required to run them. Dependencies can be Fastq files, Accession numbers or any one of the already available workflows. These dependencies will them be used to guide the user when applying workflows to their strains.


Workflows in the INNUENDO Platform are separated into two types: Classifier and Procedure.

  • Classifier - Procedure to classify non-computing required processes. Used for classification of processes prior to data analysis. Not currently implemented in the INNUENDO Platform.
  • Procedure - A procedure is a workflow that can be applied to a strain and run on the data associated to that strain.

Currently, only Procedures can be applied to strains.

Workflow Recipes

For the INNUENDO Platform, there are a set of Workflow recipes that can be constructed to run software on the strain data in the correct order. They depend on the created protocols which in the examples below they have the same name as their Nextflow Tags.

  • Reads Download:
    • Protocols (1):
      • reads_download
  • Serotyping:
    • Protocols (1):
      • seq_typing
  • Pathotyping:
    • Protocols (1):
      • patho_typing
  • INNUca:
    • Protocols (10):
      • integrity_coverage
      • fastqc_trimmomatic
      • true_coverage
      • fastqc
      • check_coverage
      • spades
      • process_spades
      • assembly_mapping
      • pilon
      • mlst
  • chewBBACA:
    • Protocols (1):
      • chewbbaca
      • Protocol Parameters:
        • schema: chewbbaca_schema_folder_name
  • Abricate:
    • Protocols (1):
      • abricate
  • SISTR:
    • Protocols (1):
      • sistr