Merge branch 'helene.rimbert-master-patch-23301' into 'master'

Update README.md

See merge request !8

README.md

@@ -191,7 +191,18 @@ This will allow to have at most 32 subproccess run through the SLURM scheduler w
 
 You can use a custom [cluster.json](cluster.json) JSON file do setup the parameters of SBATCH for each rules, and use it with with:    
 ```console
-$ snakemake -j 32 -u cluster.json --cluster "sbatch -J {cluster.jobName} -c {cluster.c} --mem {cluster.mem} -e {cluster.error} -o {cluster.output} -p debug" --verbose"
+$ snakemake -j 32 --cluster-config cluster-hpc2.json --cluster "sbatch -J {cluster.jobName} -c {cluster.c} --mem {cluster.mem} -e {cluster.error} -o {cluster.output} -p gdec" --verbose"
+```
+
+The pipeline comes with conda environment file which can be used by Snakemake. To enable the use of conda:
+```console
+$ snakemake --use-conda -j 8 --cluster-config cluster-hpc2.json --cluster "sbatch -p {cluster.partition} -c {cluster.c} -N 1 -t {cluster.time} -J {cluster.jobName} --mem={cluster.mem} -e {cluster.error} -o {cluster.output}" 
+```
+
+It is possible to force Snakemake to wait for a defined amount of time in case of latency on the filesystem of your cluster/server.
+```console
+# wating 30 seconds after each job to check for output files
+$ snakemake --latency-wait 30 [...]
 ```
 
 You can generate the diagram of all the processes and dependancies of you analysis: