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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.

Element type: CASAVAFilter


ParameterDescriptionDefault valueParameter in Workflow FileType
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 fileout-modenumeric
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.

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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