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biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing
MIT License
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Add MaskShortReads and OverrideCycles to Settings section #41

Closed ElDeveloper closed 2 years ago

ElDeveloper commented 2 years ago

These two values are needed now that we've moved away from bcl2fastq to bclconvert. These changes have been documented in the sample sheet specification and should make its way out in the 2021.09 revision.

ElDeveloper commented 2 years ago

@charles-cowart @antgonza this should be ready for review/merge.

charles-cowart commented 2 years ago

@ElDeveloper Thanks Yoshiki! I can review it tomorrow.

ElDeveloper commented 2 years ago

Thanks!

On Oct 21, 2021, at 11:14 PM, Charles Cowart @.***> wrote:

@ElDeveloper Thanks Yoshiki! I can review it tomorrow.

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ElDeveloper commented 2 years ago

These were the two settings that we added when we needed to support bclconvert instead of bcl2fastq.

On Oct 22, 2021, at 5:14 AM, Charles Cowart @.***> wrote:

@charles-cowart approved this pull request.

Thanks Yoshiki! Everything looks good. Would you mind elaborating on these two sample-sheet settings? ('MaskShortReads', 'OverrideCycles')? Ty!

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antgonza commented 2 years ago

@ElDeveloper, so do we need to parse them and use them as flags here?

ElDeveloper commented 2 years ago

No, because these aren't CLI parameters anymore. The only way to tell the conversion software to use these parameters is through the sample sheet. So we should be good.

On Oct 22, 2021, at 7:35 AM, Antonio Gonzalez @.***> wrote:

@ElDeveloper, so do we need to parse them and use them as flags here?

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charles-cowart commented 2 years ago

@ElDeveloper Thanks Yoshiki!