HarryHung
commented
4 months ago @Phuong-Le Thanks for the suggestion, your presumption is correct.
That line was an ugly workaround to address workflow.container not working when more than one container/image is being used in the workflow back then: https://github.com/nextflow-io/nextflow/issues/1758
It seems the issue has been fixed now:
- https://github.com/nextflow-io/nextflow/issues/3394
- https://github.com/nextflow-io/nextflow/commit/96ab8a69a64f4cbf0274514cbb41b839956512a8
First Nextflow stable release includes this fix is v23.10.0
I will:
- Update the code for Singularity preflight check
- Update the code for creating Docker Compose in
initsubworkflow - Update the code that provides image/container information
- Update
nextflowMinVersionto23.10
Regarding making a repo for it, I can consider that. Side note, I personally prefer using git subtree to ensure git clone still work as expected for typical users.
Phuong-Le
https://github.com/sanger-bentley-group/gps-pipeline/blob/fcbcece2c278fa56792850a68f1325f6c6246089/main.nf#L32
@HarryHung thanks very much for sharing your code. A good idea to predownload images prior to running workflows.
Here, it seems that you're searching the first config file for a 'container' flag. However, if someone else were to adopt this and run with multiple config files, this would be quite unstable.
Nextflow seems to have the
workflow.containervariable that would be useful in this case?Better still, I think the preflight code deserves its own git repo, so you can use it in multiple pipelines with something like a
git submodule. Would this be something you're interested in? Let's discuss this further?