Skip to content
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

Better handle assets dir in nf-core section #480

Merged
merged 5 commits into from
Nov 22, 2024
Merged

Better handle assets dir in nf-core section #480

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
d9982be
Update assets tip to use NXF_HOME
pinin4fjords Nov 22, 2024
3851247
set nxf_home in gitpod too
pinin4fjords Nov 22, 2024
b15051a
clarify default
pinin4fjords Nov 22, 2024
d833b95
Update docs/hello_nextflow/09_hello_nf-core.md
pinin4fjords Nov 22, 2024
7a0bef3
correct gitpod dir
pinin4fjords Nov 22, 2024
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
2 changes: 2 additions & 0 deletions .gitpod.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,8 @@ tasks:
command: docker pull -q nextflow/rnaseq-nf

- name: Start Nextflow Tutorial
env:
NXF_HOME: "/workspace/gitpod/.nextflow"
command: |
cd hello-nextflow
source $HOME/.bashrc
Expand Down
4 changes: 2 additions & 2 deletions docs/hello_nextflow/09_hello_nf-core.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -63,10 +63,10 @@ However nf-core is the largest open curated collection of Nextflow pipelines.

!!!tip

One detail that sometimes trips people up is that the pipelines you pull this way are stored in a hidden assets folder:
Pulled pipelines are stored in a hidden assets folder. By default, this folder is `$HOME/.nextflow/assets`, but in this training environment the folder has been set to `$NXF_HOME/assets`:

```bash
tree $HOME/.nextflow/assets/ -L 2
tree $NXF_HOME/assets/ -L 2
```

```console title="Output"
Expand Down
Loading