Hi @Adam_Rivers,
I have no better luck with the update too. Tested on qiime2-2018.11 and qiime2-2019.1.
Installing collected packages: q2-itsxpress
Found existing installation: q2-itsxpress 1.7.2
Uninstalling q2-itsxpress-1.7.2:
Successfully uninstalled q2-itsxpress-1.7.2
Successfully installed q2-itsxpress-1.7.3
When I export the trimmed sequences I got:
"Exported paired-end-demux.trim.qza as SingleLanePerSamplePairedEndFastqDirFmt to directory TEST"
The resulting MANIFEST is still:
sample-id,filename,direction
mock-24,mock-24_0_L001_R1_001.fastq.gz,forward
(I'm testing with mock24 in mockrobiota database)
Thanks
Luca