Use new, slimmer sometimes, containers #762
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This reverts commit 74527c8.
allyhawkins
approved these changes
May 23, 2024
| @@ -138,7 +138,7 @@ process filter_sce { | |||
| } | |||
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| process genetic_demux_sce { | |||
| container params.SCPCATOOLS_CONTAINER | |||
| container params.SCPCATOOLS_SLIM_CONTAINER | |||
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I can't comment on it, but I think for process cellhash_demux_sce you need the Seurat container?
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Yeah, I think I wasn't sure if that had everything we need, but we might as well give it a shot!
Co-authored-by: Ally Hawkins <[email protected]>
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Closes #760
This PR adds the new scpcaTools containers which upgrade everything to R 4.4.0 and Bioconductor 3.19. I tried to use the slimmest container I could find for each task, and I think I got them all correct, but a bit more testing will be required to be sure that all code paths are tests (which is what #761 is for!)
Before merging these into
mainwe will need to cut a release of scpcaTools to fix the docker versions, which are currently set toedge.