That went quick. Individual paired-end or single-end inputs, with or without the adaptor clip, both ran successfully. Collection paired, compressed or uncompressed fastq, also ran successfully.
I did notice that there are two versions of the tool on the https://usegalaxy.eu server. I used:
Use: FASTQ Quality Control >> Trimmomatic flexible read trimming tool for Illumina NGS data (Galaxy Version 0.36.5)
This older version should probably be avoided and might be what is causing problems. It is several revisions/changes/bugfixes behind the current version that works.
Avoid: FASTA/FASTQ > Trimmomatic flexible read trimming tool for Illumina NGS data (Galaxy Version 0.32.3)
ping @hxr about the duplicated/outdated tool visible in tool panel at eu server
@Lena_Ho Thanks for reporting the issue, give the updated tool a try, and see if that works for you. Will save data