ewels commented 4 months ago

Seqera Containers: Proof of concept No. 1

Hardcode container URIs at pipeline level.

Workflow for generating:

Keep conda spec in modules up to date
When pulling updates modules into a pipeline, run nextflow inspect commands to regenerate pipeline-level config files with pinned container names

Workflow for usage: (same as current except different profile names)

Online
- Use nextflow run -profile seqera_containers_docker (profile names up for refinement). Add profiles singularity and/or arm as required.
Offline
- Use nf-core download as done currently, may need some kind of profile change, not sure.

Put the config into separated files at pipeline level to keep them out of the way.

Added comments at the top of the files mentioning that it's auto-generated, along with the command used.

pditommaso commented 4 months ago

IMO, config generation should be done at the pipeline level.

ewels commented 4 months ago

IMO, config generation should be done at the pipeline level.

Yup, in this one it is pipeline level 👍🏻 Updated the PR comment a little to make this clearer.

pditommaso commented 4 months ago

Understand. I was confused by the includeConfig 👍