Conversation
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Contributor
There was a problem hiding this comment.
Pull request overview
This pull request fixes incorrect file format handling for the IMScores data in the SPACEMARKERS process. The changes ensure that the file is correctly saved as an RDS file using saveRDS() and that the output declaration references the correct filename.
Key changes:
- Fixed the output file path from
spaceMarkers.rdstoIMScores.rdsto match the actual file being generated - Corrected the file writing method from
write.csv()tosaveRDS(), aligning the function with the.rdsfile extension
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
This pull request updates the output file handling for the
SPACEMARKERSprocess innextflow/main.nf, specifically changing how theIMScoresdata is saved and referenced throughout the workflow. The main changes are focused on improving consistency and correctness in file formats and outputs.Output file handling improvements:
spaceMarkersScoresnow emits the${prefix}/IMScores.rdsfile instead of the previous${prefix}/spaceMarkers.rds, ensuring the correct file is referenced downstream.IMScoresdata is now saved as an RDS file usingsaveRDS()instead of being written as a CSV withwrite.csv(), aligning the output format with the.rdsextension and typical R conventions.