Skip to content

Update offline usage docs #3196

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 6 commits into
base: main
Choose a base branch
from
Open

Update offline usage docs #3196

Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
fe8ec0d
Update offline.md
fellen31 Mar 14, 2025
7619a5d
Update offline.md
fellen31 Mar 14, 2025
edcbe71
Update offline.md
fellen31 Mar 14, 2025
13278d1
Update offline.md
fellen31 Mar 14, 2025
4c9a20b
Merge branch 'main' into update-offline-docs
mashehu Jun 17, 2025
7f726fe
Merge branch 'main' into update-offline-docs
mashehu Jun 17, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 4 additions & 5 deletions sites/docs/src/content/docs/usage/Getting_started/offline.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,13 +35,12 @@ We do this by installing it locally on a machine that _does_ have an internet co
To run a pipeline offline, you need the pipeline code, the software dependencies, and the shared nf-core/configs configuration profiles.
We have created a helper tool as part of the _nf-core_ package to automate this for you.

On a computer with an internet connection, run `nf-core pipelines download <pipeline>` to download the pipeline and config profiles.
Add the argument `--container singularity` to also fetch the singularity container(s).
On a computer with an internet connection, run `nf-core pipelines download <pipeline>` to download the pipeline.
Add the argument `--container-system singularity` to also fetch the singularity container(s), and the argument `--download-configuration yes` to also include configuration profiles.

The pipeline and requirements will be downloaded, configured with their relative paths, and packaged into a `.tar.gz` file by default.
This can then be transferred to your offline system and unpacked.
The pipeline and requirements will be downloaded. If you used `--download-configuration yes` or `--container-system singularity` together with `container-cache-utilisation copy` the pipeline will be configured with the relative configuration and singularity image paths. However if you defined a shared Singularity image download folder, this configuration will be wrong. With `--compress tar.gz` the files can be packaged into a `.tar.gz` archive. This can then be transferred to your offline system and unpacked.

Inside, you will see directories called `workflow` (the pipeline files), `config` (a copy of [nf-core/configs](https://github.com/nf-core/configs)), and (if you used `--container singularity`) a directory called `singularity`.
Inside, you will see a directory named after the selected release or branch (e.g. `3_5_1` or `dev`) which contains the pipeline files, `configs` (a copy of [nf-core/configs](https://github.com/nf-core/configs) if you used `--download-configuration yes`), and a directory called `singularity-images` (if you used `--container-system singularity` and did't specify another shared singularity image download folder).
The pipeline code is adjusted by the download tool to expect these relative paths, so as long as you keep them together it should work as is.

To run the pipeline, simply use `nextflow run <download_directory>/workflow [pipeline flags]`.
Expand Down
Loading