Molmed / checkQC

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
http://checkqc.readthedocs.io/
GNU General Public License v3.0
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DEVELOP-2147: Add support for Miseq Nano and Micro #102

Closed matrulda closed 2 years ago

matrulda commented 2 years ago

This PR adds support for special MiSeq flowcells (nano and micro) that generates less data than the standard one.

@mikaelamo It would be nice if you could review the changes in config.yaml since you are familiar with INS-00123. :)

codecov[bot] commented 2 years ago

Codecov Report

Base: 0% // Head: 0% // No change to project coverage :thumbsup:

Coverage data is based on head (b187598) compared to base (e44042e). Patch has no changes to coverable lines.

:exclamation: Current head b187598 differs from pull request most recent head b0f4f56. Consider uploading reports for the commit b0f4f56 to get more accurate results

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matrulda commented 2 years ago

Thanks @mikaelamo and @Aratz for the reviews :pray: ! @Aratz if you could just check the last commit to make sure I didn't introduce anything weird, I think we are good to go.

Aratz commented 2 years ago

Looks good, great job :+1:

Aratz commented 2 years ago

Also I just noticed Python is now introducing match statements in version 3.10, so I guess in the future this will become the canonical way of writing this kind of code.

matrulda commented 2 years ago

Good input @Aratz, I'm not sure how to handle the >= 14 condition using match case though. :thinking: Do you have an idea? Otherwise I think I'll keep it like this.

Aratz commented 2 years ago

I'd write case x if x >= 14:, but I think it's good as it is now, we don't use Python 3.10 yet do we?

matrulda commented 2 years ago

Ah ofc, thanks, @Aratz ! I went ahead and upgraded to py3.10 since it required very few changes.

matrulda commented 2 years ago

Hmm, I had to update the ubuntu version for travis to be able to download py3.10. We should make sure that we can install py3.10 on the biotanks before including those changes in the next release.

matrulda commented 2 years ago

I removed the py3.10 commits, our old servers can't handle py3.10. Will add those changes in a separate PR so that we can release these changes first.