Maaslin3 code cleanup #1
Merged
Conversation
This file contains 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
|
Hi @sagun98 Looks great to me! Thank you for getting everything in this one PR! I am going to loop in Will to make sure we don't overlap with any work he is doing today. Hi @WillNickols This change makes the command line mode compatible with R standards and Bioconductor. I think with these changes the "require" warnings should not be present. However, if they are we can explain that the "require" (to install/load packages) would never happen unless the user is running from the command line. In short, it makes the command line option from maaslin2 totally okay! When it makes sense in your dev timeline, please merge this PR in. Thank you! |
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Outdated suggestions cannot be applied.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.
1: Changed for loop for all R files in the folder it just loops through the list ("fit.R", "utility_scripts.R","vis.R")
2: Take all of the following for loops + condense them + move them to R/maaslin3.R#L47.