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expose minOverlap parameter #117
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An important note, as part of the update to 1.10 or the R package, the Maybe it is still worth exposing this, but the maximum benefit here is very low, as one should never go below |
thanks @benjjneb ! I was not aware of that change.
I agree, probably not a priority but we have had a number of users ask about this so it may be worthwhile to give control.
we can set 4 as the minimum overlap; an error will be raised if users try to go lower. (an explanation can be given in the description) |
If it's sufficiently requested then OK. Would it be possible to create a milestone linked to the next Q2 release? |
I have added to the 2019.7 release project page — we have been using projects to organize release goals (and release dates and details are available on that page). We have not been using the milestones feature, but you are welcome to use that feature if it helps you organize issues for q2-dada2. Thanks! |
I'm gamely interested in working on this issue. EDIT: The |
Exposing the |
Ill check into this and see whats going on with the tests. |
Adding a few more options to the q2-dada2 plugin - R script which is running when calling the q2-dada2 plugin - can be easy and lead to a fine-tuned /state-of-the art dada2 pipeline whitin qiime2. In addition to the Last one, adding the possibility to export plots from the I can help to add those options if you agree they are helpfull. |
'truncQ' is almost always a superfluous parameter in my experience.
I hope to have a pull request to add pseudo-pooling up today, sadly probably too late for the imminent release though. The read length stats and |
So I started on this but my MacAir wont run the tests due to not enough RAM ...:coffin: |
Improvement Description
exposing minOverlap would allow adjustment of this parameter, which has been a bit of a bugbear for some users.
Current Behavior
minOverlap is hardcoded at 20
Proposed Behavior
Expose minOverlap but leave the default=20
References
forum xref
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