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Merge pull request #3 from AustralianBioCommons/v1.3-updateinfrastructure_optimisation
Update to v1.3
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‎infrastructure_optimisation.md‎

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# Infrastructure usage and benchmarking
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---
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## Summary
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## Exemplar 1: e.g. *Genus species* reference genome assembly
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```
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Any exemplar notes, or benchmarking, can be documented here.
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```
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## Exemplar 2: e.g. *Genus species* reference genome assembly
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```
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Any exemplar notes, or benchmarking, can be documented here.
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```
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---
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# Acknowledgements / citations / credits
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‎workflows.md‎

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[workflow name]
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===========
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- [Description](#description)
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- [Diagram](#diagram)
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- [User guide](#user-guide)
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- [Quick start guide](#quick-start-guide)
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- [Infrastructure usage and
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recommendations](#infrastructure-usage-and-recommendations)
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- [Compute resource usage across tested
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infrastructures](#compute-resource-usage-across-tested-infrastructures)
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- [Benchmarking](#benchmarking)
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- [Workflow summaries](#workflow-summaries)
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- [Metadata](#metadata)
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- [Component tools](#component-tools)
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- [Required (minimum)
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inputs/parameters](#required-minimum-inputsparameters)
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- [Additional notes](#additional-notes)
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- [Help/FAQ/Troubleshooting](#helpfaqtroubleshooting)
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- [3rd party Tutorials](#3rd-party-tutorials)
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- [Licence(s)](#licences)
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- [Acknowledgements/citations/credits](#acknowledgementscitationscredits)
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# Description
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Table with embedded registry links.
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```
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## Workflow summary
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---
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# Diagram
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```
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Example table below
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Logical visual description of processing steps for workflow
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```
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|metadata field | workflow_name / workflow_version |
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|-------------------|:---------------------------------:|
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|Version | workflow_version |
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|Maturity | stable |
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|Creators | workflow_author_1 |
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|Source | NA |
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|License | NA |
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|Workflow manager | NextFlow |
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|Container | None |
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|Install method | Manual |
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|GitHub | NA |
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|bio.tools | NA |
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|BioContainers | NA |
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|bioconda | NA |
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## Component tools
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---
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# User guide
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## Quick start guide
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```
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Example below
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General guide for deployment across multiple infrastructures (distinct from specific infrastructure quick start guide)
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```
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| Workflow element | Workflow element version | Workflow title |
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|-------------|:--------:|:--------:|
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|Tool 1 | See workflow version | workflow_name |
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|Tool 2 | See workflow version | workflow_name |
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|Tool 3 | See workflow version | workflow_name |
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---
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## Required (minimum) inputs/parameters
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## Infrastructure usage and recommendations
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```
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The minimum inputs required for the workflow to run.
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+ link to installation instructions for each infrastructure
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+ recommendations
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Documentation for a specific infrastructure should go into a infrastructure documentation template
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https://github.com/AustralianBioCommons/doc_guidelines/blob/master/infrastructure_optimisation.md
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```
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## Third party tools / dependencies
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---
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## Compute resource usage across tested infrastructures
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```
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Any dependencies should be noted here
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Table with high level compute resource usage information for standalone runs or testing of specific versions on specific computational infrastructures.
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```
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| Title | Version | Sample description | Wall time | Cores | Peak RAM in GB (requested) | Drive (GB) | HPC-HTC | If HPC-HTC is other, specify | Scheduler | Year-Month |
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| ----- | ------- | ------------------ | --------- | ----- | -------------------------- | ---------- | ------- | ---------------------------- | --------- | ---------- |
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| | | | | | | | | | | |
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# Diagram
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# Benchmarking
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Logical visual description of processing steps for workflow
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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).
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# Infrastructure specific documentation & testing
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# Workflow summaries
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## High level compute resource usage
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## Metadata
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```
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Table with high level compute resource usage information for specific versions and infrastructures.
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Example table below
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| Title | Version | Sample description | Wall time | Cores | Peak RAM in GB (requested) | Drive (GB) | HPC-HTC | If HPC-HTC is other, specify | Scheduler | Year-Month |
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|-------|---------|--------------------|-----------|-------|-------|-------|-------|-------|-------|-------|
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||||||||||||
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|metadata field | workflow_name / workflow_version |
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|-------------------|:---------------------------------:|
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|Version | workflow_version |
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|Maturity | stable |
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|Creators | workflow_author_1 |
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|Source | NA |
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|License | NA |
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|Workflow manager | NextFlow |
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|Container | None |
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|Install method | Manual |
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|GitHub | NA |
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|bio.tools | NA |
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|BioContainers | NA |
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|bioconda | NA |
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---
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## Infrastructure specific install, usage & optimisation
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## Component tools
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```
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Instructions for a specific infrastructure should go into a infrastructure documentation template
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https://github.com/AustralianBioCommons/doc_guidelines/blob/master/infrastructure_optimisation.md
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Example below
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```
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| Workflow element/tool name | Workflow element/tool version | Workflow element/tool dependencies | Workflow title |
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|--------------------------|-----------------------------|----------------------------------|----------------|
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|Tool 1 |See workflow version |Dependency/version |workflow_title |
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|Tool 2 |See workflow version |Dependency/version |workflow_title |
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|Tool 3 |See workflow version |Dependency/version |workflow_title |
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---
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# Benchmarking
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## Required (minimum) inputs/parameters
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Benchmarking for a specific infrastructure should go into a benchmarking template.
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Currently in development!!!
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The minimum inputs required for the workflow to run.
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```
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# Help / FAQ / Troubleshooting
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# Help/FAQ/Troubleshooting
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---
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## 3rd party Tutorials
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# 3rd party Tutorials
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# Licence(s)
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# Acknowledgements / citations / credits
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# Acknowledgements/citations/credits
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```
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Any attribution information that is relevant to the workflow being documented.

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