qza_to_phyloseq may ignore first row of sample metadata if it is formatted according to Qiime2's documentation about qiime2r HOT 3 CLOSED

Thanks for identifying this issue. I apparently did not do adequate vetting on this new functionality as it should be able to handle any qiime compliant metadata file. I will try to fix this up in the near future. In the meanwhile, you can always import the objects separately and build the phyloseq object yourself.

from qiime2r.

I forgot to update this, I added a read_q2metadata() function for read these these tables!

from qiime2r.

The function read_q2metadata() does not work for metadata tables without a second row (error: Metadata does not define types (ie second line does not start with #q2:types)).

Traditional qiime format metadata tables required the SampleID column as "#SampleID". Is there a way to make qza_to_phyloseq() read rownames allowing first column rowname to begin with "#"?

from qiime2r.