From 79e3dd65a753f69b17b9f7f4c043b73ed4030619 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Wed, 21 Apr 2021 11:06:39 +0200 Subject: [PATCH] Apply suggestions from code review Co-authored-by: Pontus Freyhult --- docs/uppmax.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/uppmax.md b/docs/uppmax.md index 621448b..1cf8690 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -13,7 +13,9 @@ Before running the pipeline you will need to either install Nextflow or load it To use, run the pipeline with `-profile uppmax` (one hyphen). This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers. It will enable Nextflow to manage the pipeline jobs via the Slurm job scheduler. -Using this profile, Docker image(s) containing required software(s) will be downloaded, and converted to Singularity image(s) before execution of the pipeline. +Using this profile, Docker image(s) containing required software(s) will be downloaded, and converted to Singularity image(s) if needed before execution of the pipeline. + +Recent version of Nextflow also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images. Images for some nf-core pipelines are available under `/sw/data/ToolBox/nf-core/` and those can be used by `NXF_SINGULARITY_CACHEDIR=/sw/data/ToolBox/nf-core/; export NXF_SINGULARITY_CACHEDIR`. In addition to this config profile, you will also need to specify an UPPMAX project id. You can do this with the `--project` flag (two hyphens) when launching nextflow.