Expanded README.

README.md

+# Snakemake workflows used in Germano Cecere's team
+
 This repository contains snakemake workflows to deal with (mainly _C. elegans_)
 high throughput sequencing data.
 
@@ -15,3 +17,31 @@ To get them, you need to do more stuff after cloning this repository:
     # https://stackoverflow.com/a/55570998/1878788
     git submodule update --init --remote --merge
 
+
+## Running the workflows
+
+The workflows are implemented using snakemake. They need a configuration file.
+Unfortunately, no examples are available here yet. We'll work on this, sorry
+for the inconvenience.
+
+See the `*-seq/*.snakefile` workflow descriptions as well as the
+`run_pipeline.sh` wrapper.
+
+
+## Singularity container
+
+The `singularity` subdirectory contains recipes to build a singularity
+container where the workflows are installed together with their dependencies
+and wrappers. The container needs to be built on a Linux system, and requires
+admin privileges (See `singularity/Makefile`).
+
+It currently does not include genome and annotation files, but may still
+provide a less painful experience than having to manually install all
+dependencies of the workflows.
+
+
+## Citing
+
+If you use these tools, please cite the following papers:
+
+> Barucci et al, 2020 (doi: [10.1038/s41556-020-0462-7](https://doi.org/10.1038/s41556-020-0462-7))