Reads in FASTQ file produced by CASAVA 1.8 contain 'N' or 'Y' as a part of an idetifier. 'Y' if a read if filtered, 'N' if the read if the read is not filtered. The workflow cleans up the filtered reads.
Workflow Sample Location
The workflow sample "CASAVA FASTQ Filter" can be found in the "Custom Elements" section of the Workflow Designer samples.
The workflow looks as follows: