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mycobactopia-org / MTBseq-nf

MTBSeq made simple and easy using Nextflow and nf-core standard.
https://doi.org/10.5281/zenodo.5498063
MIT License
8 stars 1 forks source link

Add multiqc report #87

Closed Mxrcon closed 1 month ago

Mxrcon commented 1 month ago

Hey, 👋

As discussed on our meetings I'm adding the code so far for multiqc report generation, I'l like to kindly request for a code review as well as a test on your side.

I'm happy to hear your thoughts on this one, Kindly, Davi

abhi18av commented 1 month ago

Thank you so much Davi, I'll take this for spin today with nf-nomad cluster to see how is the overall experience and performance :)

Mxrcon commented 1 month ago

@abhi18avm Hey :wave: I'd like to re-request your review on this PR, I've tested it again, but my delay was caused by conda configuration inconsistencies that I had to trackback and fix. Perhaps, we were only testing it using docker. I'm waiting for your input on this one. Kindly, Davi

abhi18av commented 1 month ago

Thanks @Mxrcon , I'm on it now.

abhi18av commented 1 month ago

Finally, after iterations on the MultiQC report config and the python script for preparing the MTBseq reports for MultiQC we have successfull run :)

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For NORMAL mode

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Mxrcon commented 1 month ago

Thank you @abhi18av, on our next I'd like to understand more your changes to the channel handling, certainly those changes were beyond my nextflow skill and would be nice to learn how you figured out the best setup for the channels.

abhi18av commented 1 month ago

@Mxrcon , apologies I'd be in a different meeting this week so I'll cancel.

Instead, I'll highlight the main changes in this PR itself and when we meet, we can discuss the parts which were not intuitive.