I seem to have found a bug importing CasavaOneEightLanelessPerSampleDirFm format data.
I found a workaround, but thought you should be aware of the bug so it can be fixed.
My original sample names are in this format:
I was able to import them with this code:
qiime tools import
The import works, but if I try to do anything downstream I get an error.
I then noticed that after import, within the .qza artifact data, all of the filenames have been renamed with a lane number inserted.
eDNA468_S1_R2_001.fastq.gz becomes eDNA468_S1_L001_R2_001.fastq.gz upon import
In the manifest file all of the filenames are the same as they were originally
For example: eDNA468,eDNA468_S1_R2_001.fastq.gz,reverse
Thus there is a mismatch between the sample names and the manifest withing the .qza artifact.
If I change the sample names in the manifest file to match the changed sample names manually (by adding the lane # L001 to each sample). I can get all of the downstream analyses to run fine.
It would be nice however, if the bug was fixed so that the sample names are not changed upon import when importing in this format.