Repository navigation
feat(stage): republish upstream outputs so the chain survives - #26
Merged
Merged
Conversation
Nextflow hands each process only the previous one's /results, so a stage that does not republish what it received removes it from the chain. The packaging stage needs every stage's data_process.json and the refined reconstructions, and the resample stage needs refinement/final-voxel and final-world for the specimen pass. The old capsules each had their own carry-forward helpers, which had already drifted apart; this is one tested implementation. Files are hardlinked with a copy fallback, so passing a multi-gigabyte tree along costs little.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Nextflow hands each process only the previous one's
/results, so a stage that does not republish what it received removes it from the chain.Without this the pipeline breaks in two places: the resample stage loses
refinement/final-voxelandfinal-world(so the specimen pass silently skips), and the packaging stage loses the upstreamdata_process.jsonrecords and the refined reconstructions.The old capsules each had their own carry-forward helpers, which had already drifted apart. This is one tested implementation, used by both. Files are hardlinked with a copy fallback, so passing a multi-gigabyte tree along costs little beyond directory entries.
Tests: 114 passed, 100% coverage, ruff and interrogate clean.