Updating manual

README.rst

@@ -41,7 +41,7 @@ Clone the git repository
         python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
 
 Install frangiPANe tool
----------------
+=======================
 
 Choose only one mode
 """""""""""""""""
@@ -76,7 +76,7 @@ Download or build the singularity container in the container directory
     singularity build frangiPANe.sif frangiPANe.def
 
 Checking if frangiPANe has been correctly installed
-"""""""""""""""""
+=======================
 
 ::
 
@@ -121,7 +121,7 @@ Checking if frangiPANe has been correctly installed
 
 
 II - Downloading a dataset to test frangiPANe
-=======================
+####################
 
 ::
 
@@ -129,17 +129,18 @@ II - Downloading a dataset to test frangiPANe
 
 
 III - Run FrangiPANe
-=======================
+####################
 
-**local mode**
+local mode
+=======================
 
 ::
 
     frangiPANe -e
     frangiPANe run_local -c frangiPANe/install_files/config.yaml --threads 2
 
-**cluster mode**
-
+Cluster mode
+=======================
 ::
     module load python/3.8.12
 
@@ -168,7 +169,7 @@ III - Run FrangiPANe
 
 
 IV - Outputs
-=======================
+####################
 
 ::
 
@@ -197,14 +198,14 @@ IV - Outputs
 
 
 Authors
-=======================
+####################
 
 * For version 2.0: *Sebastien Ravel and Christine Tranchant-Dubreuil (2024).*
 
 * For version 0.1: *Christine Tranchant-Dubreuil and al. (2023). FrangiPANe, a tool for creating a panreference using left behind reads. NAR Genom Bioinform. doi: 10.1093/nargab/lqad013.*
 
 Licence
-=======================
+####################
 
 -  Licencied under CeCill-C
    (http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html) and
@@ -215,6 +216,6 @@ Licence
 -  Copyright 2024
 
 Reference
-=======================
+####################
 
 .. [1] Christine Tranchant-Dubreuil and al. (2023). FrangiPANe, a tool for creating a panreference using left behind reads. NAR Genom Bioinform. doi: 10.1093/nargab/lqad013..