From 5775355e4474ed8120739ac598b6d070e3597b40 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Marius=20Bj=C3=B8rnstad?= <pmb@fa2k.net>
Date: Wed, 26 Jul 2023 10:44:37 +0200
Subject: [PATCH] Add documentation about running offline

---
 docs/usage.md | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/docs/usage.md b/docs/usage.md
index 5b7f7aa69..1d8a923b9 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -393,3 +393,26 @@ We recommend adding the following line to your environment to limit this (typica
 ```bash
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
+
+### Running the pipeline without Internet access
+
+The pipeline and container images can be downloaded using [nf-core tools](https://nf-co.re/docs/usage/offline).
+Here is an example command to download pipeline version 1.1.0 with singularity images:
+
+```
+nf-core download \
+    --container singularity \
+    --compress none \
+    --revision 1.1.0 \
+    raredisease
+```
+
+Contrary to the paragraph about Nextflow on the nf-core tools page, it is not possible to use the "-all" packaged version of Nextflow. The online version of nextflow is necessary to support the nextflow plugins used for this pipeline. Download instead the file called just `nextflow`. Nextflow will download its dependencies when it is run. Additionally, you need to download the nf-validation plugin explicitly:
+
+```
+./nextflow plugin install nf-validation@0.3.1
+```
+
+Now you can transfer the `nextflow` binary as well as its directory `$HOME/.nextflow` to the system without Internet access, and use it there.
+
+For running offline, you of course have to make all the reference data available locally, and specify `--fasta`, etc., see [above](#reference-files-and-parameters).