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hubmapconsortium / codex-pipeline

CODEX data processing code
GNU General Public License v3.0
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Group CPU pipeline steps #22

Closed mruffalo closed 3 years ago

mruffalo commented 3 years ago

This allows convenient execution of everything before and after Cytokit on general-purpose compute nodes, not GPU nodes. This seems to work well, both with manual execution of the three "stages" of the pipeline, and by using the outer pipeline.cwl wrapper, but this still seems like it could use an extra set of eyes.

VasylVaskivskyi commented 3 years ago

Looks great. The only thing I would change is naming of the subworkflows. It was confusing for me at first. For example to me illunination_stitching_1 implies that there is also illumination_stitching_2. I would change it to illumination_first_stitching

mruffalo commented 3 years ago

Renamed -- thanks!