fix merging

README.md

@@ -129,8 +129,7 @@ or how the files are processed via:
 
 ### Use the pipeline on differents snakemake version
 
-Since snakemake version 8, some things changed in the way of executing snakemake and the use of cluster configuration files are not supported anymore. Therefore use of profiles to do the workflow configuration on a cluster have been extended. This pipeline have been developped to work on either snakemake version 7 and version 8. Please take in note that you have to install plugin according to your computing cluster. Profiles are usefull because it lighten what you write on your command line, by specifying snakemake argument directly
-to a `config.yaml` file.
+Since snakemake version 8, some things changed in the way of executing snakemake and the use of cluster configuration files are not supported anymore. Therefore use of profiles to do the workflow configuration on a cluster have been extended. This pipeline have been developped to work on either snakemake version 7 and version 8. Please take in note that you have to install plugin according to your computing cluster. Profiles are usefull because it lighten what you write on your command line, by specifying snakemake argument directly to a `config.yaml` file.
 
 ### Snakemake version 8
 
@@ -474,15 +473,19 @@ intersectionApproach:
 
 ```
 
-To run the pipeline, the correct Snakefile (Snakefile_noCTL) should be used:
+To run the pipeline, the correct Snakefile (Snakefile_noCTL.smk) should be used:
 
 
+<<<<<<< HEAD
 `snakemake -s Snakefile_noCTL.smk --use-apptainer --apptainer-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1`
 
 
 or using Snakemake Profile:
 
 `snakemake -s Snakefile_noCTL.smk --workflow-profile profile/`
+=======
+`snakemake -s Snakefile_noCTL.smk --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1`
+>>>>>>> 6541328aef7a6535be7fba6a630f83dc48a610c1
 
 
 ### ATAC-seq mode  
@@ -504,6 +507,7 @@ Then fill the [config_atac.yaml](https://gitlab.pasteur.fr/hub/ePeak/-/blob/mast
 All the other features of the standard epeak pipeline are still available (preprocessing including specific quality control, peak annotation and differential analysis, etc.).
 
 
+<<<<<<< HEAD
 To run the pipeline, the correct Snakefile (Snakefile_atac.smk) should be used:
 
 
@@ -512,11 +516,19 @@ To run the pipeline, the correct Snakefile (Snakefile_atac.smk) should be used:
 or using Snakemake Profile:
 
 `snakemake -s Snakefile_atac.smk --workflow-profile profile/`
+=======
+To run the pipeline, the correct Snakefile (Snakefile_atac) should be used:
+
+
+`snakemake -s Snakefile_atac.smk --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1`
+>>>>>>> 6541328aef7a6535be7fba6a630f83dc48a610c1
 
 
 
 ## Run the pipeline on test data 
 
+Note that this data is only compatible with Snakefile and Snakefile_noCTL, but not with the ATAC pipeline (for the time being).
+
 You need to have sra-toolkit installed before to download test data.
 
 ```
@@ -653,6 +665,7 @@ Run it in a cluster environment via this standard command line:
 ---
 # Authors
 
+<<<<<<< HEAD
 * Rachel Legendre (@rlegendr), Research engineer Institut Pasteur
 * Maëlle Daunesse, Research engineer Institut Pasteur
 * Adrien Pain, Research engineer Institut Pasteur
@@ -666,7 +679,18 @@ Run it in a cluster environment via this standard command line:
 * Meije Mathé, Rouen University M2 student
 * Victoire Baillet, Research engineer Institut Pasteur
 
+=======
+* Rachel Legendre (@rlegendr), Institut Pasteur Paris
+* Maëlle Daunesse, Institut Pasteur Paris
+* Adrien Pain, Institut Pasteur Paris
+* Hugo Varet, Institut Pasteur Paris
+* Claudia Chica, Institut Pasteur Paris
+>>>>>>> 6541328aef7a6535be7fba6a630f83dc48a610c1
+
+# Contributors
 
+* Luc Jouneau, INRAE, Jouy-en-Josas
+* Amina Alioua, intern M2 Institut Pasteur Paris
 
 # How to cite ePeak ?