importing demultiplexed fastq.gz files without barcode identifier in filenames

[SoilRotifer (Mike Robeson)]

This is because that format has a specific naming schema, as outlined here.

Also, see:

Problem importing fastq.gz files after quality Trimming with cutadapt

Hi @sleva88, welcome to :qiime2:! I think the names of your files, e.g. C1_S43_L001_R1_001_trimmed.fastq end up violating the naming schema for Casava. I think if you remove _trimmed from the file names it should work. Alternatively, you can leave the files named as they are and try the Manifest format. -Mike