CASAVA FASTQ Filter Element
Reads in a FASTQ file produced by CASAVA 1.8 contain ‘N’ or ‘Y’ as part of an identifier. ‘Y’ indicates a read is filtered, ‘N’ indicates the read is not filtered. The workflow cleans up the filtered reads.
Element type: CASAVAFilter
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Output directory | Select an output directory. Custom – use “Custom directory”. Workflow – use internal directory. Input file – use input file directory. | Input file | out-mode | numeric |
| Custom directory | Specify the output directory if “Custom” is selected. | custom-dir | string | |
| Output file name | Name of the output file. If empty, the name of the first file with an added extension will be used. | out-name | string |
Input/Output Ports
| Port Name (GUI) | Workflow File Name | Slots |
|---|---|---|
| Input File | in-file | Source URL → url (string) |
| Output File | out-file | Source URL → url (string) |