as in the tsv just maps barcodes to samples but you do not have a separate barcode sequence file?
choose your own adventure:
Where are your barcodes?
- in-line with the sequences
a. see the q2-cutadapt tutorial - in the header line or some place else
a.
QIIME 2 does not have a way to handle this right now (or maybe ever? this is an unusual format) 
b. figure out a way to extract barcodes from the headers into a separate file (qiime1 had a way to do this I think)
c. import and process as EMP.