diff --git a/docs/hello_nextflow/03_hello_containers.md b/docs/hello_nextflow/03_hello_containers.md index 824372b295..9f2fc73455 100644 --- a/docs/hello_nextflow/03_hello_containers.md +++ b/docs/hello_nextflow/03_hello_containers.md @@ -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 ``` @@ -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: @@ -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. @@ -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:_ @@ -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 @@ -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: