ENH: `trim-alignment`, add `--p-addfragments` flag when using primer search option.

bokulich-lab / RESCRIPt

REference Sequence annotation and CuRatIon Pipeline

BSD 3-Clause "New" or "Revised" License

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ENH: `trim-alignment`, add `--p-addfragments` flag when using primer search option. #173

Closed mikerobeson closed 4 months ago

mikerobeson commented 5 months ago

The trim-alignment action should use, by default (?), the --p-addfragments option. The reason is outlined in the help text for qiime alignment mafft-add:

--p-addfragments / --p-no-addfragments Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used.

mikerobeson commented 4 months ago

I had not noticed this earlier, but this option is already present here. 🤦‍♂️

Closing this non-issue.