Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Sequences sampled today are incorrectly removed (filtered) #553

Closed
jameshadfield opened this issue Feb 14, 2021 · 0 comments · Fixed by #554
Closed

Sequences sampled today are incorrectly removed (filtered) #553

jameshadfield opened this issue Feb 14, 2021 · 0 comments · Fixed by #554
Labels
bug Something isn't working

Comments

@jameshadfield
Copy link
Member

Current Behavior
Sequences with a sampling date the same as the analysis day are incorrectly filtered by rule filter

Expected behavior
They shouldn't be removed.

Possible solution

Short term: add one day to the code here: https://github.com/nextstrain/ncov/blob/master/workflow/snakemake_rules/main_workflow.smk#L263 to allow

Long term: Change augur filter to keep sequences with the same date as the provided --max-date argument.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Don't filter samples collected today nextstrain/ncov
1 participant
@jameshadfield