Hello @Nicholas_Bokulich
I just tried that code you suggested and I received this:
(qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path raw_reads/ --input-format SingleEndFastqManifestPhred33V2 --output-path qiime2-raw-reads.qza
There was a problem importing raw_reads/:
raw_reads is not a file.
If you look further in the import_failure file you can see all the other iterations I've tried including:
--type SampleData[PairedEndSequencesWithQuality]
--type SampleData[SequencesWithQuality]
--format-type FastqGzFormat
--format-type SingleEndFastqManifestPhred33
--format-type SingleEndFastqManifestPhred33V2
--format-type SingleLanePerSampleSingleEndFastqDirFmt
for the manifest file I do have all three headings (sample-id, absolute-path, direction) and I've tried typing all that information in by hand in the text editor and making is simple text. I've tried tabs, spaces, commas with spaces, commas without spaces. I've tried typing it in excel and saving it as text from excel, saving it as a .csv, saving it as a .tsv and none of those have worked.