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chanzuckerberg / idseq-workflows

Portable WDL workflows for IDseq production pipelines
https://idseq.net/
MIT License
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Add 2bp wiggle room to ivar primer trimming for tailedseq protocol #105

Closed katrinakalantar closed 3 years ago

katrinakalantar commented 3 years ago

Issue: The tailedseq protocol results in some primer offset that was observed by scientists at CZB developing the protocol. This resulted in failure to trim all expected primers for samples processed using this "wet lab protocol".

Solution: This PR leverages the ivar trim primer offset parameter (-x) to allow for 2bp wiggle room associated with primer trimming for the tailedseq protocol (dependent on the input .bed file). Using 2bp wiggle room appeared to resolve the issues while limiting the impact on coverage.

Testing/verification: The trimming allowance was tested on real data for initial validation, run by the CZB scientists for verification, and an associated unit test was added.

katrinakalantar commented 3 years ago

@kislyuk I was able to rebase and the lint errors are resolved and the tests all pass now! (however, it looks like I changed way more files than I did for this PR).