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biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing
MIT License
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OverrideCycles is invalid for iSeq #67

Closed wasade closed 2 years ago

wasade commented 2 years ago

This entry specifically. It should not be included in the output sheet if the instrument is the iSeq

charles-cowart commented 2 years ago

@wasade Just to confirm, https://github.com/biocore/metagenomics_pooling_notebook/blob/826feddeb5cdf538e357cfd0980d25b203078b4e/metapool/sample_sheet.py#L61 (MaskShortReads) is still a positive addition?

wasade commented 2 years ago

I'm not sure, sorry. It was problematic when we were rapidly trying to process an iSeq run but I don't have more information. Jeff (forgot his handle) or @antgonza, do you know?

antgonza commented 2 years ago

Both need to be removed when using iSeq.

charles-cowart commented 2 years ago

Thanks guys. It seems like the definitive way to determine if the run was an iSeq run is to examine the run-id. However this info isn't usually given in the sample-sheet or the prep-sheet. Do you guys know of an alternative? Otherwise it seems like I might have to force the user to supply a run-id or isIseq parameter at KLSampleSheet creation time.

RodolfoSalido commented 2 years ago

We specify the sequencing platform during KLSampleSheet creation time.

On Apr 12, 2022, at 12:12 PM, Charles Cowart @.***> wrote:

Thanks guys. It seems like the definitive way to determine if the run was an iSeq run is to examine the run-id. However this info isn't usually given in the sample-sheet or the prep-sheet. Do you guys know of an alternative? Otherwise it seems like I might have to force the user to supply a run-id or isIseq parameter at KLSampleSheet creation time.

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charles-cowart commented 2 years ago

@RodolfoSalido Ah thank you! I did not notice sequencer was added as a parameter to make_sample_sheet(). I'll add it to the docstring.

antgonza commented 2 years ago

Fixed here: https://github.com/biocore/metagenomics_pooling_notebook/pull/71