diff --git a/README.md b/README.md index 5ea7a14e7e19993c22b5f8b68b5f8657312f8fab..52fd24d6f03439b680262877da2f02b233636072 100644 --- a/README.md +++ b/README.md @@ -1,27 +1,15 @@ -# RNAflow +<img align="left" width="100" height="100" src="images/RNAflow_logo.png" alt="RNAflow"> -[](https://snakemake.readthedocs.io/en/stable/) [](https://www.python.org/downloads/release/python-360/) +# RNAflow: A snakemake-based pipeline for standard transcriptmic analysis +[](https://snakemake.readthedocs.io/en/stable/) [](https://www.python.org/downloads/release/python-360/) +## Table of content -## Authors - -* Rachel Legendre (@rlegendr) +[[_TOC_]] -## Contributors - -* Adrien Pain -* Claudia Chica -* Elise Jacquemet -* Emeline Perthame -* Emmanuelle Permal -* Hélène Lopez-Maestre -* Hugo Varet -* Natalia Pietrosemoli -* Victoire Baillet -* Vincent Guillemot -## What is RNAflow ? +# What is RNAflow ? RNAflow is a snakemake pipeline dedicated to standard transcriptomic analysis [@Hub of Bioinformatics & Biostatistics](https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/). @@ -31,7 +19,7 @@ Be careful, RNAflow was mainly developped to run on the HPC of Institut Pasteur, <img src="images/rulegraph.svg" width="1000"> -## How to install RNAflow ? +# How to install RNAflow ? You need to install: @@ -58,9 +46,9 @@ In addition to above tools, you need to install pipeline-related tools: For Institut Pasteur HPC users, these tools are not required, they will be automatically loaded via module during pipeline running via the snakemake `--use-envmodules` instruction. -## How to run RNAflow ? +# How to run RNAflow ? -### Usage +## Usage * **Step 1: Install workflow** @@ -132,7 +120,7 @@ run it in NNCR using environment modules via -### Use case for human (or Eukaryotic) experiment +## Use case for human (or Eukaryotic) experiment - Genome information @@ -203,7 +191,7 @@ Why counting with Salmon and not STAR ? some informations here : -### Use case for host-pathogen experiment +## Use case for host-pathogen experiment - Genome information @@ -278,7 +266,7 @@ Other tools are set to 'no' -### Use case for bacteria (or prokaryotic) experiment +## Use case for bacteria (or prokaryotic) experiment - Genome information @@ -337,3 +325,23 @@ feature_counts: ``` Other tools are set to 'no' + + + + +## Authors + +* Rachel Legendre (@rlegendr) + +## Contributors + +* Adrien Pain +* Claudia Chica +* Elise Jacquemet +* Emeline Perthame +* Emmanuelle Permal +* Hélène Lopez-Maestre +* Hugo Varet +* Natalia Pietrosemoli +* Victoire Baillet +* Vincent Guillemot \ No newline at end of file diff --git a/images/RNAflow_logo.png b/images/RNAflow_logo.png new file mode 100644 index 0000000000000000000000000000000000000000..58b0155ecbfb26567405ce76075666b11cd664bb Binary files /dev/null and b/images/RNAflow_logo.png differ