Comments (7)
Pipelines are now merged!
from q2-dada2.
I agree that it would make sense to do this. At this stage it makes sense to focus on making functionality modular. When we have Pipeline
actions in the future, we can chain the more modular methods together for users who want the more "push button" functionality.
I'd prefer to hold off on this until after our 2017.3 release goes out, instead targeting it for 2017.6. We're pretty swamped for 2017.3. The other benefit of waiting till 2017.6 is that we plan to add Pipeline
actions in that release, so it would likely be the case that we wouldn't need to change the interface for denoise-single
and denoise-paired
. Those could become Pipeline
s (without users knowing that anything changed under the hood) and then we can add the new methods to split filtering into its own step.
from q2-dada2.
Is there a github issue somewhere that I can follow the progress of Q2 Pipelines?
from q2-dada2.
Yes! @ebolyen is actually working on that right now, and the plan is to have basic pipeline support in place for this release cycle (2017.10). Here's the issue and corresponding pull request:
qiime2/qiime2#86
qiime2/qiime2#348
from q2-dada2.
It might be nice to include the plotErrors
visualization as part of this process (of course this would require an all new viz in the plugin, but it could wrap the existing plotErrors
results). This recently came up on the forum.
from q2-dada2.
Is there an example Pipeline already implemented, or developer documentation on implementing Pipelines?
from q2-dada2.
@benjjneb, the framework section in the release notes has some light documentation. And the core-metrics
and core-metrics-phylogenetic
actions are pipelines:
Feel free to ping us on Slack also!
from q2-dada2.
Related Issues (20)
- Allow denoise-single to process either reverse or forward reads HOT 3
- Add long-read support HOT 27
- Certain ID schemes can become mixed up with barcodes during sorting HOT 3
- I've gone through tutorials and forums and still don't understand how to select the truncLen and trim parameters in dada2 HOT 1
- denoise-paired: add % merged to stats output
- expose minOverlap parameter HOT 10
- denoise-paired: expose matchIDs parameter HOT 3
- Error in sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) HOT 13
- Update denoise-paired document from minimum overlap 20 > 12nt
- Setting "allowOneOf" and "maxMismatch" parameters in q2/dada2 plugin HOT 1
- dada2 justConcatenate HOT 6
- Update to latest DADA2 for R 4.0 support HOT 1
- dada2 drops samples without reads unfiltered reads from table but not denoising stats. HOT 1
- Restructuring dada2 R/python code
- error while using dada2 in qiime2 HOT 1
- ENH: include error model plots in denoise-* output
- Importing DADA2 R rep. sequences into QIIME2 HOT 1
- Can not run qiime dada2 denoise-ccs without primers or adapters HOT 2
- Improve summary for merging paired reads HOT 4
- Add more DADA2 parameters to the wrapper HOT 3
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from q2-dada2.