Changes in doc architecture

Joon-Klaps · Joon-Klaps · commit 7075fd45b7f5 · 2025-01-15T16:10:48.000+01:00
diff --git a/assets/schemas/mapping_constraints.json b/assets/schemas/mapping_constraints.json
diff --git a/docs/CITATIONS.md b/docs/CITATIONS.md
@@ -1 +1,5 @@
+---
+hide:
+  - navigation
+---
 --8<-- "CITATIONS.md:"
diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
@@ -1,3 +1,7 @@
+---
+hide:
+  - navigation
+---
 # Contributing Guidelines
 
 Hi there!
diff --git a/docs/customisation/index.md b/docs/customisation/index.md
@@ -0,0 +1,13 @@
+---
+title: Customisation
+---
+
+The viralgenie pipeline is highly customisable, allowing you to tailor the analysis to your specific needs. This section provides information on how to customise the pipeline, including configuration options and database customisation.
+
+## [Custom Databases](databases.md)
+
+Viralgenie uses a variety of databases to analyse reads, contigs, and consensus constructs. While the default databases are sufficient for most cases, you can create custom databases if needed. This section provides guidance on how to create and use custom databases for different tools used in the pipeline. For more details, see the [databases guide](databases.md).
+
+## [Custom Tool Configuration](configuration.md)
+
+Viralgenie allows you to modify the arguments of the tools used in the pipeline by providing a custom configuration file. This can be done by copying a segment from the `modules.config` file and modifying the arguments as needed. For more details, see the [configuration guide](configuration.md).
diff --git a/docs/index.md b/docs/index.md
@@ -1,6 +1,9 @@
 ---
 title: Viralgenie
 description: A metagenomics analysis pipeline for eukaryotic viruses written in nextflow
+hide:
+  - navigation
+  - toc
 ---
 
 # ![viralgenie](images/nf-core-viralgenie_logo_dark.png#only-dark)
@@ -12,16 +15,17 @@ description: A metagenomics analysis pipeline for eukaryotic viruses written in
 
 ==}
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/Joon-Klaps/viralgenie)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/Joon-Klaps/viralgenie)
 
 [![GitHub Actions CI Status](https://github.com/Joon-Klaps/viralgenie/actions/workflows/ci.yml/badge.svg)](https://github.com/Joon-Klaps/viralgenie/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/Joon-Klaps/viralgenie/actions/workflows/linting.yml/badge.svg)](https://github.com/Joon-Klaps/viralgenie/actions?query=workflow%3A%22nf-core+linting%22)
+
 <!-- [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23viralgenie-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/viralgenie)-->
 
 ## Introduction
 
-**Viralgenie** is a bioinformatics best-practice analysis pipeline for reconstructing consensus genomes and to identify intra-host variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture.
+**Viralgenie** is a bioinformatics best-practice analysis pipeline for reconstructing consensus genomes and identifying intra-host variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture.
 
 ## Pipeline summary
 
diff --git a/docs/installation.md b/docs/installation.md
@@ -1,3 +1,7 @@
+---
+hide:
+  - navigation
+---
 # Installation
 
 Viralgenie uses Nextflow, and a [package/container management system](https://www.nextflow.io/docs/latest/container.html#containers) ([Docker](https://www.docker.com/resources/what-container/), [Singularity](https://docs.sylabs.io/guides/latest/user-guide/introduction.html) or [Conda](https://docs.conda.io/en/latest/)) so both need to be installed on the system where you launch your analysis.
diff --git a/docs/output.md b/docs/output.md
diff --git a/docs/parameters.md b/docs/parameters.md
@@ -1,3 +1,8 @@
+---
+hide:
+  - navigation
+---
+
 # Viralgenie pipeline parameters
 
 A pipeline to reconstruct consensus genomes and identify intrahost variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture.
diff --git a/docs/quickstart.md b/docs/quickstart.md
@@ -1,16 +1,20 @@
+---
+hide:
+  - navigation
+---
 # Quick Start
 
 Viralgenie needs two things:
 
  1. [Nextflow](https://www.nextflow.io/)
- 2. [Docker](https://www.docker.com/resources/what-container/) or [Singularity](https://docs.sylabs.io/guides/latest/user-guide/introduction.html) or [Conda](https://docs.conda.io/en/latest/)
+ 2. [Docker](https://www.docker.com/resources/what-container/), [Singularity](https://docs.sylabs.io/guides/latest/user-guide/introduction.html), or [Conda](https://docs.conda.io/en/latest/)
 
 ```bash
 # Install nextflow with conda
 conda install nextflow
 ```
 
-Run the pipeline with a small test dataset with docker containers:
+Run the pipeline with a small test dataset using Docker containers:
 ```bash
 nextflow run Joon-Klaps/viralgenie \
     -profile test,docker
@@ -46,36 +50,36 @@ An input file contains the paths to the fastq files and the sample names. The in
     sample3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz
     ```
 
-
 === "YAML"
 
     ```yaml title="input-samplesheet.yaml"
     - sample: sample1
-    fastq1: AEG588A1_S1_L002_R1_001.fastq.gz
-    fastq2: AEG588A1_S1_L002_R2_001.fastq.gz
+      fastq1: AEG588A1_S1_L002_R1_001.fastq.gz
+      fastq2: AEG588A1_S1_L002_R2_001.fastq.gz
     - sample: sample2
-    fastq1: AEG588A5_S5_L003_R1_001.fastq.gz
+      fastq1: AEG588A5_S5_L003_R1_001.fastq.gz
     - sample: sample3
-    fastq1: AEG588A3_S3_L002_R1_001.fastq.gz
-    fastq2: AEG588A3_S3_L002_R2_001.fastq.gz
+      fastq1: AEG588A3_S3_L002_R1_001.fastq.gz
+      fastq2: AEG588A3_S3_L002_R2_001.fastq.gz
     ```
 
 === "JSON"
+
     ```json title="samplesheet.json"
     [
         {
             "sample": "sample1",
             "fastq1": "AEG588A1_S1_L002_R1_001.fastq.gz",
-            "fastq2": "AEG588A1_S1_L002_R2_001.fastq.gz",
+            "fastq2": "AEG588A1_S1_L002_R2_001.fastq.gz"
         },
         {
             "sample": "sample2",
-            "fastq1": "AEG588A5_S5_L003_R1_001.fastq.gz",
+            "fastq1": "AEG588A5_S5_L003_R1_001.fastq.gz"
         },
         {
             "sample": "sample3",
             "fastq1": "AEG588A3_S3_L002_R1_001.fastq.gz",
-            "fastq2": "AEG588A3_S3_L002_R2_001.fastq.gz",
+            "fastq2": "AEG588A3_S3_L002_R2_001.fastq.gz"
         }
     ]
     ```
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css
@@ -12,8 +12,12 @@
     background-color: #4a6c6f;
   }
 
-  .md-nav {
-    margin-bottom: 0.9rem;
+  .md-sidebar {
+    width: 15%;
+  }
+
+  .md-grid {
+    max-width: 1440px;
   }
 
   .center {
diff --git a/docs/usage.md b/docs/usage.md
@@ -1,3 +1,7 @@
+---
+hide:
+  - navigation
+---
 # Usage
 
 Try out the pipeline right now!
diff --git a/docs/workflow/index.md b/docs/workflow/index.md
@@ -1,4 +1,6 @@
-## Workflow
+---
+title: Workflow overview
+---
 
 Viralgenie takes in a set of reads and performs 5 major analyses, each of them are explained in more detail in the following sections:
 
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -4,24 +4,24 @@ repo_url: https://github.com/Joon-Klaps/viralgenie
 site_url: https://joon-klaps.github.io/viralgenie/latest/
 
 nav:
-  - Home:
-      - "Introduction": README.md
-      - "Installation": installation.md
-      - "Usage": usage.md
-      - "Output": output.md
-      - "Citations": CITATIONS.md
+  - Home: index.md
   - Quick Start: quickstart.md
-  - Workflow:
-      - "Pipeline overview": workflow/overview.md
+  - Installation: installation.md
+  - Usage: usage.md
+  - Parameters: "parameters.md"
+  - Output: output.md
+  - Workflows:
+      - workflow/index.md
       - "Preprocessing": workflow/preprocessing.md
       - "Metagenomic diversity": workflow/metagenomic_diversity.md
       - "Assembly & Polishing": workflow/assembly_polishing.md
       - "Variant analysis & Iterative refinement": workflow/variant_and_refinement.md
       - "Consensus evaluation": workflow/consensus_qc.md
-  - Parameters: "parameters.md"
   - Customisation:
+      - customisation/index.md
       - "Databases": customisation/databases.md
       - "Configuration": customisation/configuration.md
+  - Citations: CITATIONS.md
   - Contributing: "CONTRIBUTING.md"
 
 theme:
@@ -54,14 +54,14 @@ theme:
     code: "Ubuntu Mono"
   features:
     - announce.dismiss
-    - content.action.edit
     - content.code.annotate
     - content.code.copy
     - header.autohide
     - navigation.footer
     - navigation.instant
     - navigation.sections
     - navigation.tabs
+    - navigation.indexes
     - navigation.tabs.sticky
     - navigation.top
     - navigation.tracking
diff --git a/nextflow_schema.json b/nextflow_schema.json

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`@@ -12,8 +12,12 @@`
`12`	`12`	`background-color: #4a6c6f;`
`13`	`13`	`}`
`14`	`14`
`15`		`- .md-nav {`
`16`		`- margin-bottom: 0.9rem;`
	`15`	`+ .md-sidebar {`
	`16`	`+ width: 15%;`
	`17`	`+ }`
	`18`	`+`
	`19`	`+ .md-grid {`
	`20`	`+ max-width: 1440px;`
`17`	`21`	`}`
`18`	`22`
`19`	`23`	`.center {`