Allow denoise-single to process either reverse or forward reads

[mestaki]

In some rare cases where the reverse reads are of better overall quality than the forwards, it would be convenient to be able to direct denoise-single to process the reverse reads instead of the default forward. This would just save the user from having to re-import their reverse reads separately.

[benjjneb]

This would just save the user from having to re-import their reverse reads separately.

Is this really a burden though? Correct me if I'm wrong, but to achieve this, the user just has to import the reverse reads as if they were forward reads, and then run denoise-single. My initial reaction is that seems straightforward enough for the edge case of reverse reads >> forward reads.

[mestaki]

You're certainly right that it is very straightforward and it totally would be a convenience thing only in the case of using the manifest importing. Currently I would import paired-end reads and make a decision about which reads to use after looking at the quality score plots. If I wanted to use both reads or forwards only, no problem, I carry on with denoise-single/paired. If I wanted the reverse reads however, I would have to remake the manifest file to either switch the forwards with reverse labels or include the reverse reads only, then re-import. It's no priority to be sure, just saves an extra step in the case of reverse reads.

[ebolyen]

Actually the SingleEnd types don't care if they are forward or reverse. It should be possible to simply drop the forward rows from the manifest and re-import as SingleEnd. They will be recorded as being the reverse direction, but no tooling actually cares.

If that doesn't work, then I think we should make it work better, since that's going to be a lot easier than working out a way to pass parameters to transformers.

(Right now denoise-single handles paired-end reads because there's a transformer in q2-types to convert paired-end to single-direction, where that transformer assumes you're more interested in the forward reads since it is being invoked at all.)