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waldronlab / curatedMetagenomicDataCuration

Sample Metadata Curation for curatedMetagenomicData
https://waldronlab.io/curatedMetagenomicDataCuration/
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number_bases and median_read_length #4

Closed edoardopasolli closed 6 years ago

edoardopasolli commented 6 years ago

in the "number_bases" and "median_read_length" fields some samples have "NA"

lwaldron commented 6 years ago

@schifferl I assume this is occurring in the R pipeline - can you identify why?

schifferl commented 6 years ago

@lwaldron I had another look at the template.csv file and some of the curation files, as well as the R pipeline – the cause of this issue is not readily apparent. I think it is likely due to changes that have happened over time and would be resolved in running the entire pipeline again. @edoardopasolli is there a specific dataset you are referring to?

edoardopasolli commented 6 years ago

most of the datasets are currently affected by this problem

schifferl commented 6 years ago

Since this is not a curation issue and has no identifiable cause I am going to close the issue. I know it is still an issue but it will be resolved with a unit test that checks the final data in the package against the curated metadata here (https://github.com/waldronlab/curatedMetagenomicData/issues/109).

edoardopasolli commented 6 years ago

"number_bases" and "median_read_length" fields have been fixed for all datasets. this issue can be closed definitevely.