diff --git a/docs/about.md b/docs/about.md new file mode 100644 index 000000000..eb72a7764 --- /dev/null +++ b/docs/about.md @@ -0,0 +1,59 @@ +# About + +## The team + +- Alexander Thomas +- Thomas Battenfeld +- Simon Magin +- Johannes Koester +- Folker Meyer + + + +## Tools used in UnCoVar + +This project wouldn't be possible without several open source tools and libraries: + +| Tool | Link | +| -------------- | --------------------------------------------------- | +| Altair | | +| BAMClipper | | +| BCFtools | | +| BEDTools | | +| Biopython | | +| bwa | | +| Covariants | | +| delly | | +| ensembl-vep | | +| entrez-direct | | +| fastp | | +| FastQC | | +| fgbio | | +| FreeBayes | | +| intervaltree | | +| Jupyter | | +| kallisto | | +| Kraken2 | | +| Krona | | +| mason | | +| MEGAHIT | | +| Minimap2 | | +| MultiQC | | +| pandas | | +| Picard | | +| PySAM | | +| QUAST | | +| RaGOO | | +| ruamel.yaml | | +| Rust-Bio-Tools | | +| SAMtools | | +| Snakemake | | +| sourmash | | +| SPAdes | | +| SVN | | +| Tabix | | +| Trinity | | +| Varlociraptor | | +| Vega-Lite | | +| Velvet | | +| vembrane | | diff --git a/docs/about/changelog.md b/docs/about/changelog.md deleted file mode 100644 index 9883fc8f8..000000000 --- a/docs/about/changelog.md +++ /dev/null @@ -1 +0,0 @@ - diff --git a/docs/about/license.md b/docs/about/license.md deleted file mode 100644 index 9883fc8f8..000000000 --- a/docs/about/license.md +++ /dev/null @@ -1 +0,0 @@ - diff --git a/docs/about/team.md b/docs/about/team.md deleted file mode 100644 index 11a33e3b0..000000000 --- a/docs/about/team.md +++ /dev/null @@ -1 +0,0 @@ -# Meet the Team diff --git a/docs/assets/tools.png b/docs/assets/tools.png new file mode 100644 index 000000000..bb40ba6e0 Binary files /dev/null and b/docs/assets/tools.png differ diff --git a/docs/assets/uncovar-displays.png b/docs/assets/uncovar-displays.png new file mode 100644 index 000000000..ef3ed6c89 Binary files /dev/null and b/docs/assets/uncovar-displays.png differ diff --git a/docs/dev-guide/tests.md b/docs/benchmarking.md similarity index 100% rename from docs/dev-guide/tests.md rename to docs/benchmarking.md diff --git a/docs/user-guide/configuration.md b/docs/configuration.md similarity index 100% rename from docs/user-guide/configuration.md rename to docs/configuration.md diff --git a/docs/consumer-guide/faqs.md b/docs/consumer-guide/faqs.md deleted file mode 100644 index 318b08dc2..000000000 --- a/docs/consumer-guide/faqs.md +++ /dev/null @@ -1 +0,0 @@ -# Frequently Asked Questions diff --git a/docs/consumer-guide/highlights.md b/docs/consumer-guide/highlights.md deleted file mode 100644 index 8063c946d..000000000 --- a/docs/consumer-guide/highlights.md +++ /dev/null @@ -1 +0,0 @@ -# Highlights diff --git a/docs/consumer-guide/index.md b/docs/consumer-guide/index.md deleted file mode 100644 index e720aab54..000000000 --- a/docs/consumer-guide/index.md +++ /dev/null @@ -1,11 +0,0 @@ -# Consumer Guide - -This section of the documentation is focused on data interpretation, targeting -virologists, epidemiologists and other involved scientists. General guidance for -interpreting the results produced by UnCoVar is provided - -- [Highlights](installation.md) -- [Understanding the Report](report-structure.md) -- [Viewing Lineages and Variants](customize-your-analysis.md) -- [Submission Ready Genomes](submission-ready-genomes.md) -- [FAQs](faqs.md) diff --git a/docs/consumer-guide/lineages-and-variants.md b/docs/consumer-guide/lineages-and-variants.md deleted file mode 100644 index 47812b4ac..000000000 --- a/docs/consumer-guide/lineages-and-variants.md +++ /dev/null @@ -1 +0,0 @@ -# Lineages and Variants diff --git a/docs/consumer-guide/submission-ready-genomes.md b/docs/consumer-guide/submission-ready-genomes.md deleted file mode 100644 index adff1d5f5..000000000 --- a/docs/consumer-guide/submission-ready-genomes.md +++ /dev/null @@ -1 +0,0 @@ -# Submission Ready Genomes diff --git a/docs/dev-guide/assembly.md b/docs/dev-guide/assembly.md deleted file mode 100644 index 834006ced..000000000 --- a/docs/dev-guide/assembly.md +++ /dev/null @@ -1,5 +0,0 @@ -# Assembly - -## Illumina - -## Oxford Nanopore diff --git a/docs/dev-guide/ci-cd.md b/docs/dev-guide/ci-cd.md deleted file mode 100644 index bd3fc15ee..000000000 --- a/docs/dev-guide/ci-cd.md +++ /dev/null @@ -1 +0,0 @@ -# Continuous Integration & Continuous Deployment diff --git a/docs/dev-guide/contributing.md b/docs/dev-guide/contributing.md deleted file mode 100644 index 9883fc8f8..000000000 --- a/docs/dev-guide/contributing.md +++ /dev/null @@ -1 +0,0 @@ - diff --git a/docs/dev-guide/faqs.md b/docs/dev-guide/faqs.md deleted file mode 100644 index 318b08dc2..000000000 --- a/docs/dev-guide/faqs.md +++ /dev/null @@ -1 +0,0 @@ -# Frequently Asked Questions diff --git a/docs/dev-guide/final-quality-control.md b/docs/dev-guide/final-quality-control.md deleted file mode 100644 index b0b79383a..000000000 --- a/docs/dev-guide/final-quality-control.md +++ /dev/null @@ -1 +0,0 @@ -# Final Quality Control diff --git a/docs/dev-guide/index.md b/docs/dev-guide/index.md deleted file mode 100644 index 4ca6de7cd..000000000 --- a/docs/dev-guide/index.md +++ /dev/null @@ -1 +0,0 @@ -# Developers Guide diff --git a/docs/dev-guide/initial-quality-control.md b/docs/dev-guide/initial-quality-control.md deleted file mode 100644 index ead9cb8c3..000000000 --- a/docs/dev-guide/initial-quality-control.md +++ /dev/null @@ -1 +0,0 @@ -# Inital Quality Control diff --git a/docs/dev-guide/lineage-calling.md b/docs/dev-guide/lineage-calling.md deleted file mode 100644 index d4f334a93..000000000 --- a/docs/dev-guide/lineage-calling.md +++ /dev/null @@ -1,5 +0,0 @@ -# Lineage Calling - -## Based on Genome Sequence - -## Based on Reads diff --git a/docs/dev-guide/pre-analysis.md b/docs/dev-guide/pre-analysis.md deleted file mode 100644 index f0ec50e1d..000000000 --- a/docs/dev-guide/pre-analysis.md +++ /dev/null @@ -1,3 +0,0 @@ -# Pre-Analysis - -## Sample Sheet diff --git a/docs/dev-guide/reporting.md b/docs/dev-guide/reporting.md deleted file mode 100644 index 63005c7e5..000000000 --- a/docs/dev-guide/reporting.md +++ /dev/null @@ -1,15 +0,0 @@ -# Reporting - -## Overview - -### Overview Table - -## Variant Call Details - -## Sequencing Details - -## Assembly - -## Variant Call Files - -## High Quality Genomes diff --git a/docs/dev-guide/sequence-preprocessing.md b/docs/dev-guide/sequence-preprocessing.md deleted file mode 100644 index ae9f0b4b5..000000000 --- a/docs/dev-guide/sequence-preprocessing.md +++ /dev/null @@ -1,7 +0,0 @@ -# Sequence Preprocessing - -## Trimming & Filtering - -## Contamination Removal - -## Primer Clipping diff --git a/docs/dev-guide/variant-calling.md b/docs/dev-guide/variant-calling.md deleted file mode 100644 index e28ec7cd7..000000000 --- a/docs/dev-guide/variant-calling.md +++ /dev/null @@ -1,9 +0,0 @@ -# Variant Calling - -## Candidate Identification - -### Illumina - -### Oxford Nanopore - -## Candidate Evaluation diff --git a/docs/faq.md b/docs/faq.md new file mode 100644 index 000000000..c348a19e7 --- /dev/null +++ b/docs/faq.md @@ -0,0 +1,12 @@ +# FAQ + +## Where to find the source code? + +[https://github.com/IKIM-Essen/uncovar](https://github.com/IKIM-Essen/uncovar) + +## How to execute the workflow? + +Once you have +[installed mamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html), +just follow the instructions +[here](https://snakemake.github.io/snakemake-workflow-catalog?usage=IKIM-Essen/uncovar). diff --git a/docs/getting-started.md b/docs/getting-started.md deleted file mode 100644 index 82bca5cd2..000000000 --- a/docs/getting-started.md +++ /dev/null @@ -1,25 +0,0 @@ -# Getting Started - -An introductory tutorial! - ---- - -## Installation - -## Configure a Run - -## Starting a Run - -## View Results - -## Getting Help - -See the [User Guide] for complete documentation of UnCoVar's features. - -To get help with UnCoVar, please use [GitHub issues]. - -[installation guide]: user-guide/installation.md -[faqs]: user-guide/faqs.md -[github issues]: https://github.com/IKIM-Essen/uncovar/issues -[github discussions]: https://github.com/IKIM-Essen/uncovar/discussions/ -[user guide]: user-guide/index.md diff --git a/docs/index.md b/docs/index.md index 45f0f1279..beeb8126b 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,64 +1,30 @@ -# Welcome to the Documentation of UnCoVar +# UnCoVar -- an open, extensible framework for virus genome analysis + + + + + UnCoVar Logo dark/light + [![Snakemake](https://img.shields.io/badge/snakemake-≥6.3.0-brightgreen.svg)](https://snakemake.bitbucket.io) [![GitHub actions status](https://github.com/koesterlab/snakemake-workflow-sars-cov2/workflows/Tests/badge.svg?branch=master)](https://github.com/koesterlab/snakemake-workflow-sars-cov2/actions?query=branch%3Amaster+workflow%3ATests) [![Docker Repository on Quay](https://quay.io/repository/uncovar/uncovar/status "Docker Repository on Quay")](https://quay.io/repository/uncovar/uncovar) -UnCoVar is a reproducible and scalable workflow for transparent and robust -SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting. +A Reproducible and Scalable Workflow for Transparent and Robust Virus Variant Calling and Lineage Assignment using SARS-CoV-2 as an example. + +- Using state of the art tools, easily extended for other viruses + +![UnCoVar tools](./assets/tools.png) + +- Tools and database updates for critical components via Conda + +- Built using modern design patterns with Conda and SnakeMake + +- Extensible and easy to customize -
-
-
-
-

Latest SARS-CoV-2 Lineage Assignment

-
-

- Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin molestie - neque scelerisque, bibendum nulla eget. -

-
-
-
-
-
-

Comprehensive Reporting

-
-

- Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin molestie - neque scelerisque, bibendum nulla eget. -

-
-
-
+- Customizable reporting with comprehensive visualization -
-
-
-
-

Submission Ready Genomes

-
-

- Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin molestie - neque scelerisque, bibendum nulla eget. -

-
-
-
-
-
-

Easy to Customize

-
-

- Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin molestie - neque scelerisque, bibendum nulla eget. -

-
-
-
+![UnCoVar visuals](./assets/uncovar-displays.png) -[Getting Started](getting-started/){ .md-button } -[User Guide](user-guide/){ .md-button } +- Submission Ready Genomes -[introductory tutorial]: getting-started.md -[User Guide]: user-guide/index.md diff --git a/docs/installation.md b/docs/installation.md new file mode 100644 index 000000000..b7d31ec08 --- /dev/null +++ b/docs/installation.md @@ -0,0 +1,6 @@ +# Installation + +## Installing + +## Maintenance + diff --git a/docs/consumer-guide/report-structure.md b/docs/user-guide.md similarity index 100% rename from docs/consumer-guide/report-structure.md rename to docs/user-guide.md diff --git a/docs/user-guide/create-your-analysis.md b/docs/user-guide/create-your-analysis.md deleted file mode 100644 index 89dc37345..000000000 --- a/docs/user-guide/create-your-analysis.md +++ /dev/null @@ -1 +0,0 @@ -# Create Your Analysis diff --git a/docs/user-guide/customize-your-analysis.md b/docs/user-guide/customize-your-analysis.md deleted file mode 100644 index 87104a02e..000000000 --- a/docs/user-guide/customize-your-analysis.md +++ /dev/null @@ -1 +0,0 @@ -# Customize Your Analysis diff --git a/docs/user-guide/faqs.md b/docs/user-guide/faqs.md deleted file mode 100644 index 318b08dc2..000000000 --- a/docs/user-guide/faqs.md +++ /dev/null @@ -1 +0,0 @@ -# Frequently Asked Questions diff --git a/docs/user-guide/index.md b/docs/user-guide/index.md deleted file mode 100644 index cb9952ba3..000000000 --- a/docs/user-guide/index.md +++ /dev/null @@ -1,19 +0,0 @@ -# User Guide - -Start analysing SARS-Cov-2 sequencing data with UnCoVar. - ---- - -The UnCoVar User Guide provides documentation aimed at users of UnCoVar. See -[Getting Started] for an introductory tutorial. You can jump directly to a -page listed below or use the _next_ and _previous_ buttons in the navigation -bar at the top of the page to move through the documentation in order. - -- [Installation](installation.md) -- [Configuration](configuration.md) -- [Create Your Analysis](create-your-analysis.md) -- [Share Your Results](share-your-results.md) -- [Customize Your Analysis.mds](customize-your-analysis.md) -- [FAQs](faqs.md) - -[getting started]: ../getting-started.md diff --git a/docs/user-guide/installation.md b/docs/user-guide/installation.md deleted file mode 100644 index 0547e2562..000000000 --- a/docs/user-guide/installation.md +++ /dev/null @@ -1,7 +0,0 @@ -# Installation - -A detailed guide. - ---- - -## Requirements diff --git a/docs/user-guide/share-your-results.md b/docs/user-guide/share-your-results.md deleted file mode 100644 index d16f7f8da..000000000 --- a/docs/user-guide/share-your-results.md +++ /dev/null @@ -1 +0,0 @@ -# Share Your Results diff --git a/mkdocs.yml b/mkdocs.yml index 508d4f367..4d6292ce8 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -8,40 +8,12 @@ repo_name: "" nav: - Welcome: index.md - - Getting Started: getting-started.md - - Consumer Guide: - - Overview: consumer-guide/index.md - - Highlights: consumer-guide/first-impression.md - - Understanding the Report: consumer-guide/report-structure.md - - Lineages and Variants: consumer-guide/lineages-and-variants.md - - Submission Read Genomes: consumer-guide/submission-ready-genomes.md - - FAQs: consumer-guide/faqs.md - - User Guide: - - Overview: user-guide/index.md - - Installation: user-guide/installation.md - - Configuration: user-guide/configuration.md - - Create Your Analysis: user-guide/create-your-analysis.md - - Share Your Results: user-guide/share-your-results.md - - Customize Your Analysis: user-guide/customize-your-analysis.md - - FAQs: user-guide/faqs.md - - Developer Guide: - - Overview: dev-guide/index.md - - How to Contribute: dev-guide/contributing.md - - Pre-Analysis: dev-guide/pre-analysis.md - - Initial Quality Control: dev-guide/final-quality-control.md - - Sequence Preprocessing: dev-guide/sequence-preprocessing.md - - Assembly: dev-guide/assembly.md - - Lineage Calling: dev-guide/lineage-calling.md - - Variant Calling: dev-guide/variant-calling.md - - Reporting: dev-guide/reporting.md - - Final Quality Control: dev-guide/initial-quality-control.md - - Tests: dev-guide/tests.md - - CI/CD: dev-guide/ci-cd.md - - FAQs: dev-guide/faqs.md - - About: - - Team: about/team.md - - License: about/license.md - - Release Notes: about/changelog.md + - Benchmarking: benchmarking.md + - Installation: installation.md + - User Guide: user-guide.md + - Configuration: configuration.md + - FAQs: faq.md + - About: about.md theme: name: material