Restructure docs

docs/usage.md

@@ -8,6 +8,13 @@
 
 nf-core/taxprofiler is a pipeline for highly-parallelised taxonomic classification and profiling of shotgun metagenomic data across multiple tools simultaneously. In addition to multiple classification and profiling tools, at the same time it allows you to performing taxonomic classification and profiling across multiple databases and settings per tool, as well as produces standardised output tables to allow immediate cross comparison of results between tools.
 
+In addition to this page, you can find additional usage information on the following pages:
+
+- [Tutorials](usage/tutorials.md)
+- [FAQ and Troubleshooting](usage/faq-troubleshooting.md)
+
+## General Usage
+
 To run nf-core/taxprofiler, at a minimum two you require two inputs:
 
 - a sequencing read samplesheet
@@ -123,16 +130,16 @@ nf-core/taxprofiler will automatically decompress and extract any compressed arc
 
 The (uncompressed) database paths (`db_path`) for each tool are expected to contain:
 
-- [**Bracken**:](#bracken-custom-database) output of the combined `kraken2-build` and `bracken-build` process.
-- [**Centrifuge**:](#centrifuge-custom-database) output of `centrifuge-build`.
-- [**DIAMOND**:](#diamond-custom-database) output of `diamond makedb`.
-- [**Kaiju**:](#kaiju-custom-database) output of `kaiju-makedb`.
-- [**Kraken2**:](#kraken2-custom-database) output of `kraken2-build` command(s).
-- [**KrakenUniq**:](#krakenuniq-custom-database) output of `krakenuniq-build` command(s).
-- [**MALT**](#malt-custom-database) output of `malt-build`.
-- [**MetaPhlAn**:](#metaphlan-custom-database) output of with `metaphlan --install` or downloaded from links on the [MetaPhlAn wiki](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#customizing-the-database).
-- [**mOTUs**:](#motus-custom-database) the directory `db_mOTU/` that is downloaded via `motus downloadDB`.
-- [**ganon**:](#ganon-custom-database) output of `ganon build` or `ganon build-custom`.
+- [**Bracken**:](usage/tutorials.md#bracken-custom-database) output of the combined `kraken2-build` and `bracken-build` process.
+- [**Centrifuge**:](usage/tutorials.md#centrifuge-custom-database) output of `centrifuge-build`.
+- [**DIAMOND**:](usage/tutorials.md#diamond-custom-database) output of `diamond makedb`.
+- [**Kaiju**:](usage/tutorials.md#kaiju-custom-database) output of `kaiju-makedb`.
+- [**Kraken2**:](usage/tutorials.md#kraken2-custom-database) output of `kraken2-build` command(s).
+- [**KrakenUniq**:](usage/tutorials.md#krakenuniq-custom-database) output of `krakenuniq-build` command(s).
+- [**MALT**](usage/tutorials.md#malt-custom-database) output of `malt-build`.
+- [**MetaPhlAn**:](usage/tutorials.md#metaphlan-custom-database) output of with `metaphlan --install` or downloaded from links on the [MetaPhlAn wiki](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#customizing-the-database).
+- [**mOTUs**:](usage/tutorials.md#motus-custom-database) the directory `db_mOTU/` that is downloaded via `motus downloadDB`.
+- [**ganon**:](usage/tutorials.md#ganon-custom-database) output of `ganon build` or `ganon build-custom`.
 
 > ℹ️ Click the links in the list above for short quick-reference tutorials how to generate custom databases for each tool.
 
@@ -465,13 +472,3 @@ We recommend adding the following line to your environment to limit this (typica
 ```bash
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
-
-## Troubleshooting and FAQs
-
-### I get a warning during centrifuge_kreport process with exit status 255
-
-When a sample has insufficient hits for abundance estimation, the resulting `report.txt` file will be empty.
-
-When trying to convert this to a kraken-style report, the conversion tool will exit with a status code `255`, and provide a `WARN`.
-
-This is **not** an error nor a failure of the pipeline, just your sample has no hits to the provided database when using centrifuge.

docs/usage/faq-troubleshooting.md

@@ -0,0 +1,9 @@
+# Troubleshooting and FAQs
+
+## I get a warning during centrifuge_kreport process with exit status 255
+
+When a sample has insufficient hits for abundance estimation, the resulting `report.txt` file will be empty.
+
+When trying to convert this to a kraken-style report, the conversion tool will exit with a status code `255`, and provide a `WARN`.
+
+This is **not** an error nor a failure of the pipeline, just your sample has no hits to the provided database when using centrifuge.

docs/tutorials.md → docs/usage/tutorials.md

@@ -6,10 +6,16 @@ This page provides a range of tutorials to help give you a bit more guidance on
 
 In this tutorial we will run you through a simple set up of a small nf-core/taxprofiler run.
 It assumes that you have basic knowledge of metagenomic classification input and output files.
+
+### Preparation
+
+#### Hardware
+
 The datasets used should be small enough to run on your own laptop or a single server node.
+
 If you wish to use a HPC cluster or cloud, please see the [nf-core documentation](https://nf-co.re/docs/usage/configuration#introduction) on how to make a relevant config file.
 
-### Preparation
+You will need 1.5 GB of hardrive space in total.
 
 #### Software
 
@@ -18,8 +24,6 @@ The tutorial will use Docker, however you can simply replace references to `dock
 
 #### Data
 
-The tutorial will require a minimum of 2GB hard drive space.
-
 First we will make a directory to run the whole tutorial in.
 
 ```bash
@@ -38,10 +42,6 @@ curl -O https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data
 curl -O https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_B_2.fastq.gz
 ```
 
-:::info
-The resulting FASTQ files will use 246 MB of disk space
-:::
-
 In this tutorial we will demonstrate running with three different profilers, and in one of those cases, running the same database twice but with different parameters.
 The database consists of two genomes of species known to be present in the metagenomes.
 You can download the databases for Kraken2, Centrifuge, and Kaiju with the following commands.
@@ -52,10 +52,6 @@ curl -O https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data
 curl -O https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/database/kaiju/kaiju.tar.gz
 ```
 
-:::info
-The resulting FASTQ files will use 19 MB of disk space
-:::
-
 To demonstrate that nf-core/taxprofiler can also accept databases as uncompressed folders, we can extract one of them.
 
 ```bash
@@ -75,10 +71,6 @@ A common contaminant in Illumina sequencing is a spike-in control of the genome
 curl -O https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/819/615/GCF_000819615.1_ViralProj14015/GCF_000819615.1_ViralProj14015_genomic.fna.gz
 ```
 
-:::info
-The resulting FASTQ files will use 1.9 KB of disk space
-:::
-
 ### Preparing Input
 
 #### Sample sheet