Using an image in a nextflow script

Pick one of the images below (make sure to follow the link to get the latest tag version):

• Default image: a default image covering as much as possible the software requirements of our nextflow scripts (julia, build tools, etc) docker://alexandrebouchardcote/default:0.1.3
• Blang image: to run the Blang CLI docker://alexandrebouchardcote/blang:0.0.0

then there are several ways to instruct nextflow to use it for one or all processes in a nextflow script.

For quick testing

load module apptainer
./nextflow run myNextFlowFile.nf -with-apptainer docker://alexandrebouchardcote/default:0.1.3

Integration into the script

For reproducibility, it is better to specify the docker container in the nextflow configuration files.

TODO

Logging into the container

Useful for debugging:

load module apptainer
apptainer shell docker://alexandrebouchardcote/default:0.1.3

Creating/improving an image

• Sign up to the free docker hub account.
• Download docker desktop
• Edit push.sh so that docker_username=.. matches with your docker hub username.

Then in order to create images that will work both on Apple Silicon and x86, follow these steps (from https://blog.jaimyn.dev/how-to-build-multi-architecture-docker-images-on-an-m1-mac/ )

1. Duplicate the folder default, give it a meaningful name, denoted mycontainer in the following, and modify its Dockerfile as needed
2. cd mycontainer
3. Test the build with docker build .
4. Once it works, commit and push, cd .., then ./push.sh mycontainer 0.0.0. This will tag your git and push multiplatform images to Dockerhub (so that even if you prepare the image on a mac with Apple Silicon, it will work on x86 seemlessly)

Misc tips when creating an image

• To login interactively in docker:

docker build -t temp .
docker run -ti temp:latest bash