broadinstitute / viral-pipelines

viral-ngs: complete pipelines
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parameterize more assembly knobs #457

Closed dpark01 closed 1 year ago

dpark01 commented 1 year ago

In workflow assemble_refbased: allow user to override default aligner parameters

In workflow sarscov2_illumina_full: allow user to override assemble_refbased default aligner, aligner parameters, and minimum coverage cutoffs