- Description
- Diagram
- User guide
- Benchmarking
- Workflow summaries
- Additional notes
- Help/FAQ/Troubleshooting
- 3rd party Tutorials
- License(s)
- Acknowledgements/citations/credits
Introduction of tool, including its input(s)/output(s) as well as a list (or link to) of available shell commands (useful when building interfaces/wrappers for containers)
Table with embedded registry links, if suitable.
| Repository / Registry | Available? |
|---|---|
| GitHub | ● |
| bio.tools | ● |
| BioContainers | ● |
| bioconda | ● |
Logical visual description of processing steps for tool, e.g. for pipelines shipped as packages (Falcon, Cellranger, ..)
General installation guide.
If there are different installation requirements based on infrastructures you could indicate these here, or in the individual infrastructure documentation template: https://github.com/AustralianBioCommons/doc_guidelines/blob/master/infrastructure_optimisation.md
General guide for deployment across multiple infrastructures (distinct from specific infrastructure quick start guide).
You could include:
- a link to installation instructions for each computational infrastructure
- recommendations for use on a specific computational infrastructure
Documentation for a specific infrastructure should go into a infrastructure documentation template https://github.com/AustralianBioCommons/doc_guidelines/blob/master/infrastructure_optimisation.md
Table with high level compute resource usage information for standalone runs or testing of specific versions on specific computational infrastructures.
| Tool | Version | Sample description | Wall time | Cores | Peak RAM in GB (requested) | Drive (GB) | HPC-HTC | If HPC-HTC is other, specify | Scheduler | Year-Month |
|---|---|---|---|---|---|---|---|---|---|---|
Benchmarking for a specific infrastructure should go here: if this document is complicated it should go into a benchmarking template, or be provided elsewhere (e.g. Zenodo).
Example table below - based on requirements for bio.tools
To discover appropriate EDAM ontology terms, you can use EDAM browser
bio.tools citation: Ison, J. et al. (2015). Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research. doi: 10.1093/nar/gkv1116 PMID: 26538599
EDAM citation: Ison, J., Kalaš, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S. and Rice, P. (2013). EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics, 29(10): 1325-1332.
PMID: 23479348 Open access
| metadata field | value |
|---|---|
| Tool name | |
| Description | |
| Homepage URL | |
| Software version(s) | |
| EDAM topic(s) | |
| EDAM operation(s) | |
| Maturity | |
| Creators | |
| License | |
| Container | |
| Install method | |
| GitHub | |
| bio.tools | |
| BioContainers | |
| bioconda |
The minimum inputs required for the workflow to run.
Add / list known dependencies, or link to a list of these dependencies.
Any comment on major features being introduced, or default/API changes that might result in unexpected behaviours.
Any attribution information that is relevant to the tool being documented.