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

pass/fail to include 7-gene MLST? #25

Open
lskatz opened this issue Mar 17, 2020 · 1 comment
Open

pass/fail to include 7-gene MLST? #25

lskatz opened this issue Mar 17, 2020 · 1 comment
Labels
enhancement

Comments

@lskatz
Copy link
Owner

lskatz commented Mar 17, 2020

Is your feature request related to a problem? Please describe.
7-gene MLST is used as a contamination detector. Yet, it is not included in the pass/fail portion of the report.

Describe the solution you'd like
Should be included in passfail.tsv. If a sample has > 7 alleles in its scheme, then it should be considered contaminated. Either -25% or should count as a "yes" as contaminated and simply -33% if either kraken or this module detects contamination.
@lskatz
Copy link
Owner Author

lskatz commented Aug 10, 2020

I'm labeling this one as an enhancement and will leave it alone unless there is some support for this enhancement.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
enhancement
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@lskatz