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Merge pull request #8 from AustralianBioCommons/v1.5
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Update workflows.md structure
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@supernord
supernord authored Aug 17, 2023
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- [Diagram](#diagram)
- [User guide](#user-guide)
- [Quick start guide](#quick-start-guide)
- [Required (minimum)
inputs/parameters](#required-minimum-inputsparameters)
- [Infrastructure usage and
recommendations](#infrastructure-usage-and-recommendations)
- [Compute resource usage across tested
infrastructures](#compute-resource-usage-across-tested-infrastructures)
- [Benchmarking](#benchmarking)
- [Workflow summaries](#workflow-summaries)
- [Metadata](#metadata)
- [Component tools](#component-tools)
- [Required (minimum)
inputs/parameters](#required-minimum-inputsparameters)
- [Benchmarking](#benchmarking)
- [Additional notes](#additional-notes)
- [Help/FAQ/Troubleshooting](#helpfaqtroubleshooting)
- [3rd party Tutorials](#3rd-party-tutorials)
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---

# Description

```
Introduction of workflow and its component tools.
## Description

Table with embedded registry links.
```
> Introduction of workflow and its component tools.
> Table with embedded registry links.
---

# Diagram
## Diagram

```
Logical visual description of processing steps for workflow
```

---

# User guide
## User guide

## Quick start guide

```
General guide for deployment across multiple infrastructures (distinct from specific infrastructure quick start guide)
```
### Quick start guide

---
> General guide for deployment across multiple infrastructures (distinct from specific infrastructure quick start guide)
## Infrastructure usage and recommendations

```
+ link to installation instructions for each infrastructure
+ recommendations
Documentation for a specific infrastructure should go into a infrastructure documentation template
https://github.com/AustralianBioCommons/doc_guidelines/blob/master/infrastructure_optimisation.md
```
### Install instructions

---

## Compute resource usage across tested infrastructures
### Dependencies

```
Table with high level compute resource usage information for standalone runs or testing of specific versions on specific computational infrastructures.
```

| 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 |
| ----- | ------- | ------------------ | --------- | ----- | -------------------------- | ---------- | ------- | ---------------------------- | --------- | ---------- |
| | | | | | | | | | | |
### Required (minimum) inputs/parameters

---
> The minimum inputs required for the workflow to run.
# Benchmarking

```
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).
```
### Infrastructure usage and recommendations

---
> + link to installation instructions for each infrastructure
> + recommendations
> Documentation for a specific infrastructure should go into a infrastructure documentation template
https://github.com/AustralianBioCommons/doc_guidelines/blob/master/infrastructure_optimisation.md

# Workflow summaries

## Metadata

```
Example table below
```

|metadata field | workflow_name / workflow_version |
|-------------------|:---------------------------------:|
|Version | workflow_version |
|Maturity | stable |
|Creators | workflow_author_1 |
|Source | NA |
|License | NA |
|Workflow manager | NextFlow |
|Container | None |
|Install method | Manual |
|GitHub | NA |
|bio.tools | NA |
|BioContainers | NA |
|bioconda | NA |

---
### Compute resource usage across tested infrastructures

## Component tools
> Table with high level compute resource usage information for standalone runs or testing of specific versions on specific computational infrastructures.
```
Example below
```
| Workflow element/tool name | Workflow element/tool version | Workflow element/tool dependencies | Workflow title |
|--------------------------|-----------------------------|----------------------------------|----------------|
|Tool 1 |See workflow version |Dependency/version |workflow_title |
|Tool 2 |See workflow version |Dependency/version |workflow_title |
|Tool 3 |See workflow version |Dependency/version |workflow_title |
---
| Title | Version | Sample description | Wall time | Cores | Peak RAM in GB (requested) | Drive (GB) | Compute system (e.g. Pawsey Setonix HPC, AWS) | Scheduler | Year-Month |
| ----- | ------- | ------------------ | --------- | ----- | -------------------------- | ---------- | ------- | --------- | ---------- |
| | | | | | | | | | |

## Required (minimum) inputs/parameters

```
The minimum inputs required for the workflow to run.
```
### Benchmarking

---
> 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).
# Additional notes

---
## Additional notes

# Help / FAQ / Troubleshooting

---
## Help / FAQ / Troubleshooting

# 3rd party Tutorials

---
## 3rd party Tutorials

# License(s)

---
## License(s)

# Acknowledgements/citations/credits

```
Any attribution information that is relevant to the workflow being documented.
```
## Acknowledgements/citations/credits

> Any attribution information that is relevant to the workflow being documented.
---

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