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qiime2 / q2-dada2

QIIME 2 plugin wrapping DADA2
BSD 3-Clause "New" or "Revised" License
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can `trim-left` and `trunc-len` be made optional and default to no trimming/truncation? #43

Closed gregcaporaso closed 7 years ago

gregcaporaso commented 7 years ago

related to #16

benjjneb commented 7 years ago

Making trim-left optional with a default of 0 would be appropriate right now.

Making trunc-len optional is trickier to do automatically, especially for sequencing techs that don't always have the same number of bases.

gregcaporaso commented 7 years ago

Making trunc-len optional is trickier to do automatically, especially for sequencing techs that don't always have the same number of bases.

I was thinking that it would default to not trimming.

benjjneb commented 7 years ago

The dada2 code currently requires all input sequences to be the same length, although if all goes well that requirement will be removed in our next release (1.4, March/April).

gregcaporaso commented 7 years ago

OK, we can hold off on this until then.

ebolyen commented 7 years ago

FYI: trim-left is already set to default to 0 (in the 2017.2 release).

benjjneb commented 7 years ago

I pushed variable-length support to the main devel-branch of dada2 today (cddce98a98894e4a621f6767e61fe9aaed638e06) so this feature will definitely be in the upcoming 1.4 release.

Another consequence, dada2 now works for ITS data, since trimming to a fixed length is no longer required.

ebolyen commented 7 years ago

This was resolved in #66.