From 5d2b3cae24429376f5d87aed7691b2c2ba0bd8b4 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 14 Aug 2023 15:35:42 +0930 Subject: [PATCH 1/4] Update workflows.md structure --- documentation_templates/workflows.md | 128 +++++++-------------------- 1 file changed, 30 insertions(+), 98 deletions(-) diff --git a/documentation_templates/workflows.md b/documentation_templates/workflows.md index b5cef84..333a2fd 100644 --- a/documentation_templates/workflows.md +++ b/documentation_templates/workflows.md @@ -5,16 +5,13 @@ - [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) @@ -23,131 +20,66 @@ --- -# Description +## Description -``` -Introduction of workflow and its component tools. +> Introduction of workflow and its component tools. +> Table with embedded registry links. -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 +### Required (minimum) inputs/parameters + +> The minimum inputs required for the workflow to run. + + +### Infrastructure usage and recommendations + +> + link to installation instructions for each infrastructure +> + recommendations -Documentation for a specific infrastructure should go into a infrastructure documentation template +> Documentation for a specific infrastructure should go into a infrastructure documentation template https://github.com/AustralianBioCommons/doc_guidelines/blob/master/infrastructure_optimisation.md -``` ---- -## Compute resource usage across tested infrastructures +### Compute resource usage across tested infrastructures -``` -Table with high level compute resource usage information for standalone runs or testing of specific versions on specific computational infrastructures. -``` +> 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 | | ----- | ------- | ------------------ | --------- | ----- | -------------------------- | ---------- | ------- | ---------------------------- | --------- | ---------- | | | | | | | | | | | | | ---- - -# 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). -``` +### Benchmarking ---- - -# 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 | +> 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). ---- -## Component tools +## Additional notes -``` -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 | ---- -## Required (minimum) inputs/parameters +## Help / FAQ / Troubleshooting -``` -The minimum inputs required for the workflow to run. -``` ---- +## 3rd party Tutorials -# Additional notes ---- +## License(s) -# Help / FAQ / Troubleshooting ---- +## Acknowledgements/citations/credits -# 3rd party Tutorials +> Any attribution information that is relevant to the workflow being documented. ---- - -# License(s) - ---- - -# Acknowledgements/citations/credits - -``` -Any attribution information that is relevant to the workflow being documented. -``` - ---- From 0cadba63fd988236694cdbf72e96277e4a70a279 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson <50811354+supernord@users.noreply.github.com> Date: Tue, 15 Aug 2023 12:06:14 +0930 Subject: [PATCH 2/4] Update workflows.md --- documentation_templates/workflows.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/documentation_templates/workflows.md b/documentation_templates/workflows.md index 333a2fd..dadc41e 100644 --- a/documentation_templates/workflows.md +++ b/documentation_templates/workflows.md @@ -57,9 +57,9 @@ https://github.com/AustralianBioCommons/doc_guidelines/blob/master/infrastructur > 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 | -| ----- | ------- | ------------------ | --------- | ----- | -------------------------- | ---------- | ------- | ---------------------------- | --------- | ---------- | -| | | | | | | | | | | | +| Title | Version | Sample description | Wall time | Cores | Peak RAM in GB (requested) | Drive (GB) | HPC-HTC e.g. Pawsey Setonix | Scheduler | Year-Month | +| ----- | ------- | ------------------ | --------- | ----- | -------------------------- | ---------- | ------- | --------- | ---------- | +| | | | | | | | | | | ### Benchmarking From 4d886bef468ce4dd07d59b73eff9dc9368fcb568 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson <50811354+supernord@users.noreply.github.com> Date: Tue, 15 Aug 2023 14:46:11 +0930 Subject: [PATCH 3/4] Update workflows.md --- documentation_templates/workflows.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/documentation_templates/workflows.md b/documentation_templates/workflows.md index dadc41e..9f06d26 100644 --- a/documentation_templates/workflows.md +++ b/documentation_templates/workflows.md @@ -57,7 +57,7 @@ https://github.com/AustralianBioCommons/doc_guidelines/blob/master/infrastructur > 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 e.g. Pawsey Setonix | Scheduler | Year-Month | +| 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 | | ----- | ------- | ------------------ | --------- | ----- | -------------------------- | ---------- | ------- | --------- | ---------- | | | | | | | | | | | | From 9f24dde5c4b712dad4475c709ffad312336f8158 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 17 Aug 2023 10:04:38 +0930 Subject: [PATCH 4/4] workflows.md - add install and dependency headings --- documentation_templates/workflows.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/documentation_templates/workflows.md b/documentation_templates/workflows.md index 333a2fd..967e6a6 100644 --- a/documentation_templates/workflows.md +++ b/documentation_templates/workflows.md @@ -39,6 +39,12 @@ Logical visual description of processing steps for workflow > General guide for deployment across multiple infrastructures (distinct from specific infrastructure quick start guide) +### Install instructions + + +### Dependencies + + ### Required (minimum) inputs/parameters > The minimum inputs required for the workflow to run.