6 months ago by
I had a similar issue with Trimmomatic earlier this week. I uploaded .gz files which Galaxy decompressed and identified as fastq files. Trimmomatic couldn't recognize the files when run from the tool bar - although oddly, workflows which had Trimmomatic as the first step in the process had absolutely no problems processing the fastq files. Weird.
Things like this happen to me rather frequently on Galaxy ever since I started using it several years ago - for whatever reason (whether it's the way my institute formats and compresses its fastq's or the way Galaxy decompresses and identifies file type) my fastq files are quite often in a format that many Galaxy tools have trouble recognizing. I'm not sure if I have the best workaround, but this is what I was taught to do by another Galaxy user: include a grooming step in my workflows. The "FASTQ GROOMER" tool seems to format my fastq files appropriately (they go in fastq, they come out fastqsanger) and after running the fastq files through it I never have this issue with tools working with my data. Just make sure you use the proper settings - the "FASTQ GROOMER" tool is more intended to switch between FASTQ score formats so make sure you tell the program what format your sequencing machine is scoring with or you might mess up your files.