docs: cleanup of documentation (#621)

* cleanup of documentation * docs: added name * fixed linting error * with local linter * Update about.md * fit * fmt * fmt * pin python for ragoo * rev --------- Co-authored-by: Alexander Thomas <[email protected]>
IKIM-Essen · Feb 26, 2024 · b34c995 · b34c995
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diff --git a/docs/about.md b/docs/about.md
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+# 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         | <www.doi.org/10.21105/joss.01057>                   |
+| BAMClipper     | <www.doi.org/10.1038/s41598-017-01703-6>            |
+| BCFtools       | <www.doi.org/10.1093/gigascience/giab008>           |
+| BEDTools       | <www.doi.org/10.1093/bioinformatics/btq033>         |
+| Biopython      | <www.doi.org/10.1093/bioinformatics/btp163>         |
+| bwa            | <www.doi.org/10.1093/bioinformatics/btp324>         |
+| Covariants     | <www.github.com/hodcroftlab/covariants>             |
+| delly          | <www.doi.org/10.1093/bioinformatics/bts378>         |
+| ensembl-vep    | <www.doi.org/10.1186/s13059-016-0974-4>             |
+| entrez-direct  | <www.ncbi.nlm.nih.gov/books/NBK179288>              |
+| fastp          | <www.doi.org/10.1093/bioinformatics/bty560>         |
+| FastQC         | <www.bioinformatics.babraham.ac.uk/projects/fastqc> |
+| fgbio          | <www.github.com/fulcrum-genomics/fgbio>             |
+| FreeBayes      | <www.arxiv.org/abs/1207.3907>                       |
+| intervaltree   | <www.github.com/chaimleib/intervaltree>             |
+| Jupyter        | <www.jupyter.org>                                   |
+| kallisto       | <www.doi.org/10.1038/nbt.3519>                      |
+| Kraken2        | <www.doi.org/10.1186/s13059-019-1891-0>             |
+| Krona          | <www.doi.org/10.1186/1471-2105-12-385>              |
+| mason          | <publications.imp.fu-berlin.de/962>                 |
+| MEGAHIT        | <www.doi.org/10.1093/bioinformatics/btv033>         |
+| Minimap2       | <www.doi.org/10.1093/bioinformatics/bty191>         |
+| MultiQC        | <www.doi.org/10.1093/bioinformatics/btw354>         |
+| pandas         | <pandas.pydata.org>                                 |
+| Picard         | <broadinstitute.github.io/picard>                   |
+| PySAM          | <www.doi.org/10.11578/dc.20190903.1>                |
+| QUAST          | <www.doi.org/10.1093/bioinformatics/btt086>         |
+| RaGOO          | <www.doi.org/10.1186/s13059-019-1829-6>             |
+| ruamel.yaml    | <www.sourceforge.net/projects/ruamel-yaml>          |
+| Rust-Bio-Tools | <www.github.com/rust-bio/rust-bio-tools>            |
+| SAMtools       | <www.doi.org/10.1093/bioinformatics/btp352>         |
+| Snakemake      | <www.doi.org/10.12688/f1000research.29032.1>        |
+| sourmash       | <www.doi.org/10.21105/joss.00027>                   |
+| SPAdes         | <www.doi.org/10.1089/cmb.2012.0021>                 |
+| SVN            | <www.doi.org/10.1142/s0219720005001028>             |
+| Tabix          | <www.doi.org/10.1093/bioinformatics/btq671>         |
+| Trinity        | <www.doi.org/10.1038/nprot.2013.084>                |
+| Varlociraptor  | <www.doi.org/10.1186/s13059-020-01993-6>            |
+| Vega-Lite      | <www.doi.org/10.1109/TVCG.2016.2599030>             |
+| Velvet         | <www.doi.org/10.1101/gr.074492.107>                 |
+| vembrane       | <www.github.com/vembrane/vembrane>                  |
diff --git a/docs/about/changelog.md b/docs/about/changelog.md
diff --git a/docs/about/license.md b/docs/about/license.md
diff --git a/docs/about/team.md b/docs/about/team.md
diff --git a/docs/assets/tools.png b/docs/assets/tools.png
diff --git a/docs/assets/uncovar-displays.png b/docs/assets/uncovar-displays.png
diff --git a/docs/dev-guide/tests.md → docs/benchmarking.md b/docs/dev-guide/tests.md → docs/benchmarking.md
diff --git a/docs/user-guide/configuration.md → docs/configuration.md b/docs/user-guide/configuration.md → docs/configuration.md
diff --git a/docs/consumer-guide/faqs.md b/docs/consumer-guide/faqs.md
diff --git a/docs/consumer-guide/highlights.md b/docs/consumer-guide/highlights.md
diff --git a/docs/consumer-guide/index.md b/docs/consumer-guide/index.md
diff --git a/docs/consumer-guide/lineages-and-variants.md b/docs/consumer-guide/lineages-and-variants.md
diff --git a/docs/consumer-guide/submission-ready-genomes.md b/docs/consumer-guide/submission-ready-genomes.md
diff --git a/docs/dev-guide/assembly.md b/docs/dev-guide/assembly.md
diff --git a/docs/dev-guide/ci-cd.md b/docs/dev-guide/ci-cd.md
diff --git a/docs/dev-guide/contributing.md b/docs/dev-guide/contributing.md
diff --git a/docs/dev-guide/faqs.md b/docs/dev-guide/faqs.md
diff --git a/docs/dev-guide/final-quality-control.md b/docs/dev-guide/final-quality-control.md
diff --git a/docs/dev-guide/index.md b/docs/dev-guide/index.md
diff --git a/docs/dev-guide/initial-quality-control.md b/docs/dev-guide/initial-quality-control.md
diff --git a/docs/dev-guide/lineage-calling.md b/docs/dev-guide/lineage-calling.md
diff --git a/docs/dev-guide/pre-analysis.md b/docs/dev-guide/pre-analysis.md
diff --git a/docs/dev-guide/reporting.md b/docs/dev-guide/reporting.md
diff --git a/docs/dev-guide/sequence-preprocessing.md b/docs/dev-guide/sequence-preprocessing.md
diff --git a/docs/dev-guide/variant-calling.md b/docs/dev-guide/variant-calling.md
diff --git a/docs/faq.md 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
diff --git 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
+
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://github.com/IKIM-Essen/uncovar/assets/77535027/8e17c6fc-ff7a-4c25-afc9-7888036d693e">
+  <source media="(prefers-color-scheme: light)" srcset="https://github.com/IKIM-Essen/uncovar/assets/77535027/c99f5a94-749b-422e-b319-1e3700d40a8e">
+  <img alt="UnCoVar Logo dark/light">
+</picture>
 
 [![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
 
-<div class="row">
-  <div class="column">
-    <div class="card">
-        <div class="card-title">
-            <h3>Latest SARS-CoV-2 Lineage Assignment</h3>
-        </div>
-        <p>
-            Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin molestie
-            neque scelerisque, bibendum nulla eget.
-        </p>
-    </div>
-  </div>
-  <div class="column">
-    <div class="card">
-        <div class="card-title">
-            <h3>Comprehensive Reporting</h3>
-        </div>
-        <p>
-            Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin molestie
-            neque scelerisque, bibendum nulla eget.
-        </p>
-    </div>
-  </div>
-</div>
+- Customizable reporting with comprehensive visualization
 
-<div class="row">
-  <div class="column">
-    <div class="card">
-        <div class="card-title">
-        <h3>Submission Ready Genomes</h3>
-        </div>
-        <p>
-            Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin molestie
-            neque scelerisque, bibendum nulla eget.
-        </p>
-    </div>
-  </div>
-  <div class="column">
-    <div class="card">
-        <div class="card-title">
-        <h3>Easy to Customize</h3>
-        </div>
-        <p>
-            Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin molestie
-            neque scelerisque, bibendum nulla eget.
-        </p>
-    </div>
-  </div>
-</div>
+![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
@@ -0,0 +1,6 @@
+# Installation
+
+## Installing
+
+## Maintenance
+
diff --git a/docs/consumer-guide/report-structure.md → docs/user-guide.md b/docs/consumer-guide/report-structure.md → docs/user-guide.md
diff --git a/docs/user-guide/create-your-analysis.md b/docs/user-guide/create-your-analysis.md
diff --git a/docs/user-guide/customize-your-analysis.md b/docs/user-guide/customize-your-analysis.md
diff --git a/docs/user-guide/faqs.md b/docs/user-guide/faqs.md
diff --git a/docs/user-guide/index.md b/docs/user-guide/index.md
diff --git a/docs/user-guide/installation.md b/docs/user-guide/installation.md
diff --git a/docs/user-guide/share-your-results.md b/docs/user-guide/share-your-results.md
diff --git 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