remove warning for manual component size threshold setting#305
Merged
Conversation
ptajvar
force-pushed
the
remove-component-size-threshold-warning
branch
from
bb7e31d to
6ffcab6
Compare
ptajvar
force-pushed
the
remove-component-size-threshold-warning
branch
from
6ffcab6 to
0526f0d
Compare
johandahlberg
approved these changes
Feb 12, 2026
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 subscribe to this conversation on GitHub.
Already have an account?
Sign in.
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
We have observed from a variety of cell types that setting minimum component size to 8000 UMIs is a robust threshold for cell calling. So, we are now removing the warning when the graph step is run having --component-size-min-threshold set manually.
Fixes: #PNA-1966
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Existing tests.
PR checklist: