diff --git a/docs/vsc_ugent.md b/docs/vsc_ugent.md index f13454b..b1d4fd9 100644 --- a/docs/vsc_ugent.md +++ b/docs/vsc_ugent.md @@ -19,8 +19,6 @@ module load Nextflow nextflow run -profile vsc_ugent, ``` -I also highly recommend specifying a location of a Singularity cache directory, by specifying the location with the `$SINGULARITY_CACHEDIR` bash environment variable in your `.bash_profile` or `.bashrc` or by adding it to your PBS script. If this cache directory is not specified, - All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space. The default work directory is set to `$VSC_SCRATCH_VO_USER/work` per this configuration