From 0e5045c080e23de7ab25d60cba5a7b422a2eb695 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Tue, 26 Jun 2018 15:12:17 +0200
Subject: [PATCH] Further README updates
---
README.md | 16 +++++++++++-----
1 file changed, 11 insertions(+), 5 deletions(-)
diff --git a/README.md b/README.md
index 5b8d046..34fc78e 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.
--
GitLab