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chanzuckerberg / idseq-workflows

Portable WDL workflows for IDseq production pipelines
https://idseq.net/
MIT License
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reduce the nanopore workflow min_length parameter to accommodate ClearLabs samples in the interim #96

Closed katrinakalantar closed 3 years ago

katrinakalantar commented 3 years ago

Modify the default min_length parameter for nanopore sars-cov-2 consensus genome analysis to achieve higher coverage for ClearLabs samples, which tend to have a distribution of read lengths that include a significant number (> 50%) of reads with lengths below the initial 350 parameter value.

This PR is to enable DPH users who are actively using the pipeline during the beta phase to achieve genomes of comparable quality. However, further validation and a parameter sweep will need to be done prior to v1 launch to ensure that this modification does not produce issues for standard ONT data.

katrinakalantar commented 3 years ago

Given the recent info about ClearLabs pre-filtering, I will close this PR in place of upcoming changes that will skip the ApplyLengthFilter altogether for those data.