Add container load scripts for Docker and Podman (#3634 follow up) #3706
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This was referenced Aug 13, 2025
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Docs updated in nf-core/website#3463 |
…talled and assume python instead.
JulianFlesch
approved these changes
Aug 28, 2025
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This is a follow up PR on the large
nf-core pipelines downloadrefactor PR #3634, and should be merged AFTER it.This PR replaces the load command for Docker images that is printed to the command line in #3634 with shell scripts copied to the output container folder. I've added support for both Docker and Podman. The latter one might need more testing before releasing it into the wild since we need to manually capture the image name and tag from the
manifest.jsonin the Docker image tar archive, and retag the images. My testing suggests that this approach works however.The load scripts are put inside
nf_core/pipelines/download/load_scripts/and read using theimportlib.resourcesfunction. If there is a better place to keep the files and load them please feel free to change this logic!I've tested the Docker/Podman script on
nf-core/bamtofastqby loading the images into Docker/Podman an dsubsequently running the pipeline with thetestprofile. Since the tests use thetest-datasetrepo I've not run it in a fully offline environment, but instead looked at the pull events from Docker/Podman. From what I can tell it looks to be working correctly. It would however be awesome if someone with experience running pipelines in a fully offline environment tested the scripts.For diff with the base branch see: ErikDanielsson#2
PR checklist
CHANGELOG.mdis updateddocsis updated