Update README.md

README.md

@@ -2,20 +2,47 @@
 
 Dépot de travail pour versionner le travail réalisé pendant le stage
 
-## src
+## Requirements
 
-Version actuelle du pipeline meta-consensus
+This tool uses the Conda environment manager from the Anaconda software to run.
+
+To install Conda check : https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html
 
 ## Installation
-Voir comment réaliser un installeur facile a utiliser
+
+You only need to download this repository in order to launch the pipeline, the first run will handle the setup for every tools using Conda.
 
 ## Usage
-Pour l'instant : dans un environnement avec snakemake installé:
-Avec un dossier data situé dans le dossier parent contenant les données à utiliser.
- > snakemake --use-conda -c{nb coeurs}
+usage: mc_msa.py [-h] -input INPUT -output OUTPUT [-reference REFERENCE] [-size SIZE] [-list LIST]
+                 [-tools TOOLS] [-consensus_threshold CONSENSUS_THRESHOLD]
+                 [-metaconsensus_threshold METACONSENSUS_THRESHOLD] [-depth DEPTH] [-plot PLOT]
+                 [-region_overlap REGION_OVERLAP] [-cores CORES]
+
+Creates the config file then runs the Meta-consensus pipeline
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -input INPUT          Reads file
+  -output OUTPUT        Target directory for the pipeline results
+  -reference REFERENCE  Reference for alignment and statistics
+  -list LIST            A list of regions to work on (format: [r1, r2, ...] with r1  or [rStart1_End1, rStart2_End2 ...])
+  -size SIZE            The size for cutting region (default: 2000)
+                        (default: no region)
+  -tools TOOLS          The list of tools to use in the meta-consensus (default: ['abpoa', 'spoa',
+                        'kalign2', 'kalign3', 'mafft', 'muscle'])
+  -consensus_threshold CONSENSUS_THRESHOLD
+                        Threshold(s) used for the MSA consensus step (default: [70])
+  -metaconsensus_threshold METACONSENSUS_THRESHOLD
+                        Threshold(s) used for the Meta-consensus result (default: [60])
+  -depth DEPTH          The depth used in the process (default: [60])
+  -plot PLOT            Analyse the meta-consensus and MSA consensus quality (requires reference)
+  -region_overlap REGION_OVERLAP
+                        The size of the overlap between regions
+  -cores CORES          The amount of cores to use in the pipeline run (default 1)
 
 ## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
+Flavien Lihouck
+Special thanks to Coralie Rohmer's work on the tool MSA-limit, which inspired and was used in many parts of this project.
 
 ## License
-For open source projects, say how it is licensed.
+Probably CC_BY ?