From e7edabf0f3fdb8ba0024602b46b06e603b771851 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Mon, 24 Feb 2020 18:34:42 +0100
Subject: [PATCH] Expanded README.

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 README.md | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/README.md b/README.md
index 5220934..cb05f95 100644
--- a/README.md
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+# 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))
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