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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. For example: @HWI-ST880:181:D1WRUACXX:8:1102:4905:2125 1:N:0:TAAGGG CTTACATAACTACTGACCATGCTCTCTCTTGTCTGTCTCTTATACACATCT + 111442222322324232AAFFHIJJJJJJIHIIF111CGGFHIG???FGB @HWI-ST880:181:D1WRUACXX:8:1102:7303:2101 1:Y:0:TAAGGG TCCTTACTGTCTGAGCAATGGGATTCCATCTTTTACGATCTAGACATGGCT + 11++4222322.

Parameters in GUI

ParameterDescriptionDefault value
Output directorySelect an output directory. Custom - specify the output directory in the 'Custom directory' parameter. Workflow - internal workflow directory. Input file - the directory of the input file.Input file
Custom directory

Specify the output directory.

Output file nameA name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention. 

Parameters in Workflow File 

Type: CASAVAFilter

ParameterParameter in the GUIType
out-modeOutput directorynumeric
custom-dirCustom directorystring
out-nameOutput file namestring

Input/Output Ports

The element has 1 input port:

Name in GUI: Input File

Name in Workflow File: in-file


Slot In GUISlot in Workflow FileType
Source URLurlstring

And 1 output port:

Name in GUI: Output File

Name in Workflow File: out-file


Slot In GUISlot in Workflow FileType
Source URLurlstring



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