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

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