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vinisalazar / metaphor

Metaphor: a general-purpose workflow for assembly and binning of metagenomes
https://metaphor-workflow.readthedocs.io/
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handling of blank/control samples #58

Closed ganiatgithub closed 7 months ago

ganiatgithub commented 1 year ago

Hi,

Among a list of my samples, there are two control samples that has almost no sequence reads, and therefore no subsequent intermediate files generated. It has often led to breaks, and my work around will be to adding artificial sequences to intermediates so that it doesn't affect the running of the entire workflow.

Maybe it's more effective to remove these blank samples from the samples.csv file right from the start? Seems naive, just want to post this thought.

Thanks.

vinisalazar commented 1 year ago

Yes, it's probably easier to just remove them.

I will see if I can add some error handling to deal with that.

Best, Vini

vinisalazar commented 7 months ago

I'll be closing this issue for now, but don't hesitate to reopen it if needed.