I have imported in QIIME2 my fastq files from PGM using the next command line:
qiime tools import
--type 'SampleData[SequencesWithQuality]'
--input-path manifest_file.csv
--output-path demux.qza
--source-format SingleEndFastqManifestPhred33
You have the instructions to make your manifest_file here: Importing data — QIIME 2 2018.2.0 documentation in the section "Fastq manifest formats".
After import your data you can continue doing analyses in QIIME2 (filter quality, clustering, denoising, assign taxonomy, etc....). Other option is use other program like Cutadapt to filter by quality and length, etc.) and then import the fastq filtered instead the raw files.
I hope this information will be useful for you 
Good luck!
MMC