diff --git a/docs/alice.md b/docs/alice.md index afc1342..35d1799 100644 --- a/docs/alice.md +++ b/docs/alice.md @@ -13,6 +13,8 @@ module load Nextflow/21.03.0 module load Java/11.0.2 ``` +We also highly recommend specifying a location of a cache directory to store singularity images (so you re-use them across runs, and not pull each time), by specifying the location with the `$NXF_SINGULARITY_CACHE_DIR` bash environment variable in your `.bash_profile` or `.bashrc`. + 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 completeed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space.