Merge pull request #37 from psteinb/create-logs

minor fixes adapting to behavior observed with snakemake 6.0.5

Author: Trevor Keller

_episodes/13-cluster.md

@@ -197,7 +197,7 @@ cluster: "sbatch --time={resources.time_min} --mem={resources.mem_mb}
           -e slurm/logs/{rule}_{wildcards}"
 jobs: 25
 default-resources: [cpus=1, mem_mb=1000, time_min=5]
-resources: [cpus=100, mem_mb=1000000]
+resources: [cpus=100, mem_mb=100000]
 ```
 {: .source}
 
@@ -206,14 +206,18 @@ This file has several components.
 the cluster.
 Here we've used SLURM's `sbatch` command and arguments for setting time limits
 and resources with snakemake wildcards defining the requested values.
-We've also specified where to save SLURM logs and what to call them; note that
-this folder must already exist.
+
+We've also specified where to save SLURM logs and what to call them. **Note** that
+this folder must already exist. If the folders don't exist, snakemake will hang.
+
 Values for any command line argument to snakemake can be defined in our
 profile, although a value is required (e.g. the `--use-conda` argument could be
 included in our profile with `use-conda: true`).
+
 `jobs` specifies the maximum number of jobs that will be submitted at one time.
 We also specified the `default-resources` that will be requested for each job,
 while `resources` defines the resource limits.
+
 With these parameters, snakemake will use no more than 100 cpus and 100000 MB
 (100 GB) at a time between all currently submitted jobs.
 While it does not come into play here, a generally sensible default is slightly