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Update docs/alice.md

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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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@ -13,6 +13,8 @@ module load Nextflow/21.03.0
module load Java/11.0.2 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. 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. 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.