Hi @Bernhard,
most likely your files have ‘fastq.gz’ datatype in Galaxy, eg format: fastq.gz. Cutadapt recognizes this datatype, while Trim Galore works with datatype like fastqsanger.gz. Similar topic discussed on the forum, eg Unicycler failed - "reads unavailable" -- Inputs not recognized due to an incompatible datatype assignment - #3 by vanina.guernier
Kind regards,
Igor