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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

Parameters

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.


custom-dirstring
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.
out-namestring

Input/Output Ports

The element has 1 input port:

Name in GUI: Input File

Name in Workflow File: in-file

Slots:

Slot In GUISlot in Workflow FileType
Source URLurlstring

And 1 output port:

Name in GUI: Output File

Name in Workflow File: out-file

Slots:

Slot In GUISlot in Workflow FileType
Source URLurlstring



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