Savant Batch Processing #22
Open
Conversation
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
…esults target in "all" rule.
Collaborator
Author
|
Input validation of phenotype column names should also be reviewed since filesystem paths are affected by user input. |
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Outdated suggestions cannot be applied.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 adds a new Snakefile that supports processing multiple phenotypes with a single scan through the genotype file using Savant linear model. Post-processing (plot, tophit, and filtered results) is now done in the Snakefile.
Integration of this into the Encore app will require modifications to how results are displayed for a job (e.g., a dropdown that selects which phenotype to display plots for), as well as how progress is determined.