Write docs for new version

Author: kieranr51

docs/cli-reference/extractnc.md

@@ -1,14 +1,17 @@
 # ExtractNC
 
 ```
-extarctnc [-h] genome gff_file
+usage: extract_nc [-h] [-o OUTPUT] genome gff_file
 
 positional arguments:
-  genome  	FASTA containing the genome to extract from
-  gff_file	GFF file containing annotations of CDS and mRNA regions
-
-optional arguments:
-  -h, --help  show this help message and exit
+  genome                FASTA containing the genome to extract from
+  gff_file              GFF file containing annotations of CDS and mRNA
+                        regions
+
+options:
+  -h, --help            show this help message and exit
+  -o OUTPUT, --output OUTPUT
+                        FASTA file to write output to
 ```
 
 Input files:
@@ -21,4 +24,5 @@ Output files:
 
 - `noncoding.fasta` - FASTA file containing only the transcribed noncoding regions of the DNA
 
-*Note the method used here will not work if there a coding region is labelled outside a single mRNA region. The program does a check before running to make sure this is true and throws an exception before trying to run if so, to prevent nonsense results from being produced.*
+!!! warning
+    The method used here will not work if there a coding region is labelled outside a single mRNA region. The program does a check before running to make sure this is true and throws an exception before trying to run if so, to prevent nonsense results from being produced.

docs/cli-reference/index.md

@@ -4,26 +4,24 @@ References of how to use the command line interface of the program and notes on
 General help message is as follows:
 
 ```
-usage: hlsmallrna [-h] [-q] [-C PATH_TO_CONFIG]
-              	{process,sort,extractnc,unitas,targetid,all} ...
+usage: hlsmallrna [-h] [-o OUTPUT] [-t THREADS] [-k] [-v] config_file
 
-Pipeline to process small RNAs
+Pipeline to process small RNAs - version 2
 
 positional arguments:
-  {process,sort,extractnc,unitas,targetid,all}
-	process         	Preprocessing for the RNA
-	sort            	Find RNAs that align to a genome and sort them by
-                    	length
-	extractnc       	Extract the noncoding region from a fasta with a GFF
-                    	file
-	unitas          	Run unitas on split files and merge results
-	targetid        	Align small RNA to a number of genome features to find
-                    	out what is targeted
-	all             	Run process, sort and unitas one after the other
+  config_file           Path to YAML config file
 
-optional arguments:
-  -h, --help        	show this help message and exit
-  -q, --quiet       	Suppress output from intermediate commands
-  -C PATH_TO_CONFIG, --path-to-config PATH_TO_CONFIG
-                    	Path to the TOML format config file to use
-```
+options:
+  -h, --help            show this help message and exit
+  -o OUTPUT, --output OUTPUT
+                        Directory to write output to (will be created if it
+                        doesn't exist, default: hlsmallrna_output)
+  -t THREADS, --threads THREADS
+                        Number of threads to run the pipeline on (default: 4)
+  -k, --keep-files      If set, keep the intermediate files, to help debug the
+                        application
+  -v, --verbose         If set, print the output for the intermediate commands
+```
+
+!!! note "The Config File"
+	If you are looking for instructions on writing the config file, use [the relevent page of the walkthrough](../walkthrough/config.md) to help.

docs/cli-reference/process.md

@@ -1,5 +1,46 @@
+---
+hide:
+  - navigation
+  - toc
+---
 # Welcome to the Hunt Lab Small RNA Pipeline Documentation
 
-This tool is designed to automate a lot of the common bioinformatics performed on small RNA by the [Hunt Lab](https://www.vickyhuntlab.org/). It is deliberately designed to be highly configurable so it can be easily applied to a wide range of scenarios, though most of our work is on nematode and nematomorph worms.
+This documentation is for version 2 of the pipeline, select 1.1.0 from the version dropdown for the version 1 documentation.
 
-Use the tabs above or buttons below to navigate this site.
+This is a pipeline developed in [Vicky Hunt's Lab](https://www.vickyhuntlab.org/) at the [University of Bath](https://www.bath.ac.uk), UK to analyse small RNA data in a quick and consistent way between projects. It is deliberately designed to be highly configurable so it can be easily applied to a wide range of scenarios, though most of our work is on nematode and nematomorph worms. 
+
+# Background
+
+Most of the original methodology was devised by Mona Suleiman, Dominika Lastik and Vicky Hunt for the papers below. This was then developed into a usable pipeline by Kieran Reynolds in 2022 and updated to version 2 in 2025. 
+
+> Suleiman, M., Kounosu, A., Murcott, B. et al. piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode. Sci Rep 12, 10156 (2022). [https://doi.org/10.1038/s41598-022-14247-1](https://doi.org/10.1038/s41598-022-14247-1)
+
+> Lastik, D., Kounosu, A., Dayi, M. et al. Small non-coding RNAs have predicted roles in reproductive biology and transposable element regulation in the parasitic worm Strongyloides venezuelensis. Sci Rep 15, 20608 (2025). [https://doi.org/10.1038/s41598-025-01968-2](https://doi.org/10.1038/s41598-025-01968-2)
+
+# Citation
+
+This pipeline is mainly a combination of existing tools so, doesn't have a paper attached to it but can be referenced with the repository URL and version number. For example:
+
+> This analysis was performed using HuntLab-smallRNA v2.0.0 ([https://github.com/Vicky-Hunt-Lab/HuntLab-smallRNA](https://github.com/Vicky-Hunt-Lab/HuntLab-smallRNA)).
+
+For the internal steps please cite the papers of the tools used:
+
+**Trim**:
+
+> Martin, Marcel. (2011). CUTADAPT removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 17. 10.14806/ej.17.1.200.
+
+**Sort**:
+
+> Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359 (2012). https://doi.org/10.1038/nmeth.1923 
+
+**Unitas**:
+
+> Gebert, D., Hewel, C. & Rosenkranz, D. unitas: the universal tool for annotation of small RNAs. BMC Genomics 18, 644 (2017). https://doi.org/10.1186/s12864-017-4031-9
+
+**Targetid**:
+
+> Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359 (2012). https://doi.org/10.1038/nmeth.1923
+
+**Enrich**:
+
+> Carlos P Cantalapiedra, Ana Hernández-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas, eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale, Molecular Biology and Evolution, Volume 38, Issue 12, December 2021, Pages 5825-5829, https://doi.org/10.1093/molbev/msab293