Use sambamba for duplicate marking. #1082
Open
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
We weren't using the barcode tag feature in these pipelines, but if we were we could bring back a picard version.
|
I'll let John and others review, but I support this change as one that increases the speed through parallelization while using the same duplicate marking strategy and producing essentially identical results. |
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Outdated suggestions cannot be applied.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.
In porting the FDA metrics pipelines to the WDL workflows I ran into that those had been updated to switch duplicate markers but these had not. This carries that change over to the CWL version. I haven't tried running it on the immuno.cwl yet--thought I'd open this and see if it's something we wanted to do before running a test.