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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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use ivar default of 30 for illuminaKeepLen in Sanger config #61

Closed dkj closed 4 years ago

dkj commented 4 years ago

This is more appropriate for libraries created by ligating adapters on the end of the amplicon (than when tagmentation is used as with many other Illumina pipelines)

m-bull commented 4 years ago

Thanks and good catch @dkj .

Thinking aloud, but maybe the default for this should be set dynamically based on whether we're keeping reads without primers (proxy for Nextera/Ligation).