First time posting so I hope I do this correctly. I am using galaxy locally and installed the ea-utils fastq-mcf (FastqMcf). When using the trimming options (not defaults) the -C option gets set to the -s option. I checked the fastq-mcf.xml wrapper and indeed there is an mistake on line 42. -s $trimming.sampcnt Should be -C $trimming.sampcnt I hope this helps, Cheers, Mike ________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org