Skip to content

Update 03_hello_containers.md #424

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

Merged
merged 5 commits into from
Oct 28, 2024
Merged

Update 03_hello_containers.md #424

Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
0b7d281
Update 03_hello_containers.md
pinin4fjords Oct 28, 2024
c5fb3a7
correct wrong path
pinin4fjords Oct 28, 2024
f8abae3
Exit container after example
pinin4fjords Oct 28, 2024
b93f5bc
Correct name of containers script
pinin4fjords Oct 28, 2024
3993cf3
prettier
pinin4fjords Oct 28, 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
16 changes: 11 additions & 5 deletions docs/hello_nextflow/03_hello_containers.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ Notice that the prompt has changed to `(base) root@b645838b3314:/tmp#`, which in
If we run:

```console title="Output"
(base) root@b645838b3314:/tmp# ls
(base) root@b645838b3314:/tmp# ls /
bin dev etc home lib media mnt opt proc root run sbin srv sys tmp usr var
```

Expand Down Expand Up @@ -115,7 +115,7 @@ One way to do this is to **mount** a **volume** from the host system into the co
Prior to working on the next task, confirm that you are in the `hello-nextflow` directory.

```bash
cd /workspace/gitpod/nf-training/hello-nextflow
cd /workspace/gitpod/hello-nextflow
```

Then run:
Expand Down Expand Up @@ -166,6 +166,12 @@ Output:
/_]' /_]'
```

Now exit the container once again:

```bash
exit
```

### Takeaway

You know how to pull a container and run it interactively, make your data accessible to it, which lets you try commands without having to install any software on your system.
Expand All @@ -183,7 +189,7 @@ This means that you can use any container image you like to run your processes,

### 2.1. Add a container directive to your process

Edit the `hello_containers.nf` script to add a `container` directive to the `cowsay` process.
Edit the `hello-containers.nf` script to add a `container` directive to the `cowsay` process.

_Before:_

Expand All @@ -207,7 +213,7 @@ process cowSay {
Run the script to see the container in action.

```bash
nextflow run hello_containers.nf
nextflow run hello-containers.nf
```

!!! NOTE
Expand Down Expand Up @@ -410,7 +416,7 @@ Doing these exercises is _not required_ to understand later parts of the trainin
|| ||
```

### 4.1. Modify the `hello_containers.nf` script to use a getQuote process
### 4.1. Modify the `hello-containers.nf` script to use a getQuote process

We have a list of computer and biology pioneers in the `containers/data/pioneers.csv` file.
At a high level, to complete this exercise you will need to:
Expand Down
Loading