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

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