From ad83430632d14762f08d7e1c6e45550cb403d225 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B8rn=20Peare=20Bartholdy?= <47455812+bbartholdy@users.noreply.github.com> Date: Tue, 28 Sep 2021 12:43:54 +0200 Subject: [PATCH] Update docs/alice.md Co-authored-by: James A. Fellows Yates --- docs/alice.md | 2 ++ 1 file changed, 2 insertions(+) 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.