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 in GUI
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Output directory | Select 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 | out-mode | numeric |
| Custom directory | Specify the output directory. |
| custom-dir | string | |
| Output file name | A 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
...
| out- |
...
| name |
...
| string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input File
Name in Workflow File: in-file
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Source URL | url | string |
And 1 output port:
Name in GUI: Output File
Name in Workflow File: out-file
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Source URL | url | string |