diff --git a/README.md b/README.md index 5b8d0460080ef72478c91e9996bea76b2312dc44..34fc78ee7010955e1202eae60afa214a71d2b9ec 100755 --- a/README.md +++ b/README.md @@ -158,23 +158,29 @@ In case you do not have Conda yet, it is easiest to just install 3. Run `snakemake` - - -## Cluster support +## Snakemake recommendations You can ask Snakemake to submit your jobs to a HPC cluster. We provided a config file (`cluster.json`) for this purpose, yet it might need to be adapted to your -infrastructure. +infrastructure. Here is an example command: ``` snakemake -j 100 \ --cluster-config Snake.cluster.json \ --cluster "sbatch --cpus-per-task {cluster.n} --time {cluster.time} --mem {cluster.mem}" ``` + + Further, it is often advisable to increase the time Snakemake waits for the + file system via this flag: + + ``` + --latency-wait 60 + ``` + Finally, of course the cluster mode can be combined with `--use-singularity`. -## Provide SNV calls +## SNP calls The pipeline will run simple SNV calling using [samtools](https://github.com/samtools/samtools) and [bcftools](https://github.com/samtools/bcftools) on Strand-seq. If you **already have SNV calls**, you can avoid that by entering your VCF files into the pipeline.