Report format

[llk578496]

Hi @mattdmem ,

Thank you for creating wf-16s. As this succeeds Epi2me FASTQ 16S, could wf-16s generate reports matching Epi2me's format?

Producing an Epi2me-style report would be appreciated to integrate smoothly into our existing downstream processes. Please advise if this is possible or provide examples of specifications needed.

We're eager to use wf-16s advances while allowing continuity. Thank you for your time.

Regards, Eddie

[mattdmem]

Hi @llk578496,

Thanks for your interest in the workflow. What is it about the old EPI2ME reports that you need that the new ones don't provide? Unfortunately we aren't going to be providing legacy style reports, but we can consider adding features to the new ones.

Matt

[llk578496]

We would like to request for adding barcode filtering to the wf-16s abundance section. In Epi2me, we could filter abundances by sample. This allowed individual reports like below.

However, wf-16s currently combines abundances across all samples in a batch.

Barcode filtering in wf-16s would restore our ability to examine taxa distributions at the sample level. Thank you for any help on this request.

[mattdmem]

@nggvs is going to add a parameter to adjust abundance thresholds per sample - will that be helpful?

[nggvs]

Hi @llk578496 , Are you still interested in having this feature?

[llk578496]

Hi @nggvs ,

Sure! We will be grateful if you could add this feature.

Adding barcode filtering and individual csv export with taxa sorted by abundance would be great for the reporting. Also, It will be great if these csv could be exported by default.

Thanks you very much!

[nggvs]

Hi @llk578496 , I take note on this and will consider this option for future releases. Just to make sure this is what you are interested in:

• Individual CSVs (better if they are also in the output directory) for each sample sorted by abundances I'm not sure of what you would like as barcode filtering? Could you explain that with more detail?

Thank you for using the pipeline!

[llk578496]

Being able to filter results and see abundances by individual barcode which similar to the handy filter in Lineages would be ideal.

Thank a lot!

[nggvs]

Hi @llk578496 , First of all thank you for your suggestions, I agree that it would make the report more convenient for some specific cases. We may provide single sample reports apart from a general one. Nevertheless I think that unfortunately is not going to be implement in the short term. However, I'll take this into account as a future feature request! Please keep making suggestions so that we can improve our workflows!