Documentation

docs/README.md

@@ -26,21 +26,13 @@ sequencing experiments - fast and simple. Whether you are an experimentalist
 struggling with large scale data analysis or an experienced bioinformatician,
 when there's RNA-seq data to analyze, just _zarp 'em_!
 
-**NOTES TO SELF:**
-
-- Include references in `/includes/references.md`
-- Include abbreviations in `includes/abbreviations.md` (example: EAWNKWIMPR)
-- Include emojis (example: :rocket:)
-- Check out the [ZARP-cli docs pages](https://zavolab.github.io/zarp-cli/)
-for inspiration.
-- Check out [MKDocs](https://www.mkdocs.org/) and [Material for
-MkDocs](https://squidfunk.github.io/mkdocs-material/) docs for more info
-
 ## How does it work?
 
-Briefly, when a _ZARP_ run is triggered, ...
+ZARP requires conda or mamba to install the basic dependencies. Each individual step of the workflow run either in its own Apptainer (Singularity) container or in its own Conda virtual environemnt.
+
+Once the installation is complete, you fill in a [config.yaml](https://github.com/zavolanlab/zarp/blob/dev/tests/input_files/config.yaml) file with parameters and a [samples.tsv](https://github.com/zavolanlab/zarp/blob/dev/tests/input_files/samples.tsv) file with sample specific installation. You can easily trigger ZARP by making a call to snakemake with the appropriate parameters.
 
-**TODO:** Complete section
+The pipeline can be executed in different systems or HPC clusters. ZARP generates multiple output files that help you QC your data and proceed with downstream analyses. Apart from running the main ZARP workflow, you can also run a second pipeline that downloads data from SRA, and a third pipeline that populates a file with the samples and determines sample specific parameters.
 
 ## How to cite
 

docs/guides/parameterization.md

@@ -4,7 +4,7 @@
 
 ZARP runs on default parameters that were chosen based on the majority of samples being analyzed. To simplify adding non-default parameters of the tools, we created a config file, which enables the user to use any of the extra parameters offered by any of the tools. These options override the default ones, unless they are essential to the correct use of the rule in which case they are considered "immutable" and will not be changed. This extra `rule_config.yaml` file enables the user to easily manipulate the parameters, without having to deal with making changes in the workflow.
 
-The entries look like the following example. The rule name is specified the parameters to customize are give.
+An example of a `rule_config.yaml` is shown below:
 
 ```bash
 remove_adapters_cutadapt:

docs/guides/usage.md

@@ -1,9 +1,12 @@
 # Execution of pipelines
 
-ZARP consists of three different pipelines. The main pipeline that processes the data, the second allows you to download the sequencing libraries from the Sequence Read Archive (SRA), and the third that populates a file with the samples and determines sample specific parameters. <p> <p>
+ZARP consists of three different pipelines. The main pipeline that processes the data, the second allows you to download the sequencing libraries from the Sequence Read Archive (SRA), and the third that populates a file with the samples and determines sample specific parameters.
 
 If you can create a `samples.tsv` file and fill in the metadata for the different sequencing experiments then the main pipeline can analyze your data.
 
+!!! info "Prerequisites"
+
+    The code below assume that you have already [installed](./installation.md) ZARP.
 
 ## How to run ZARP
 
@@ -79,7 +82,7 @@ your run.
     bash run.sh
     ```
 
-6. To find out more information on the output files please go to the [output files](https://zavolanlab.github.io/zarp/guides/outputs/) section
+6. To find out more information on the output files please go to the [output files](./outputs.md) section.
 
 
 ## How to download data from SRA?