Set Protocols¶
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¶
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
used Software¶
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:
- reads_download
- seq_typing
- patho_typing
- integrity_coverage
- fastqc (fastqc_trimmomatic)
- true_coverage
- fastqc_2 (fastqc)
- integrity_coverage_2 (check_coverage)
- spades
- process_mapping
- pilon
- mlst
- sistr
- chewBBACA
- abricate
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.
Nextflow Tags¶
Nextflow Tags are the specific names that FlowCraft requires to build Nextflow pipelines based on the available software at the INNUENDO Platform.
Below you have all the available Nextflow Tags retrieved from FLowCraft that can be used in the INNUENDO Platform:
=> reads_download
input_type: accessions
output_type: fastq
dependencies: None
=> seq_typing
input_type: fastq
output_type: None
dependencies: None
=> patho_typing
input_type: fastq
output_type: None
dependencies: None
=> integrity_coverage
input_type: fastq
output_type: fastq
dependencies: None
=> fastqc_trimmomatic
input_type: fastq
output_type: fastq
dependencies: integrity_coverage
=> true_coverage
input_type: fastq
output_type: fastq
dependencies: None
=> fastqc
input_type: fastq
output_type: fastq
dependencies: None
=> check_coverage
input_type: fastq
output_type: fastq
dependencies: None
=> spades
input_type: fastq
output_type: fasta
dependencies: integrity_coverage
=> process_spades
input_type: fasta
output_type: fasta
dependencies: None
=> assembly_mapping
input_type: fasta
output_type: fasta
dependencies: None
=> pilon
input_type: fasta
output_type: fasta
dependencies: assembly_mapping
=> mlst
input_type: fasta
output_type: fasta
dependencies: None
=> abricate
input_type: fasta
output_type: None
dependencies: None
=> chewbbaca
input_type: fasta
output_type: None
dependencies: None
=> sistr
input_type: fasta
output_type: None
dependencies: None
Protocol Name¶
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