Builds quality control reports.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| 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 |
| List of adapters | Specifies a non-default file which contains the list of adapter sequences which will be explicity searched against the library. The file must contain sets of named adapters in the form name[tab]sequence. Lines prefixed with a hash will be ignored. | |
| List of contaminants | Specifies a non-default file which contains the list of contaminants to screen overrepresented sequences against. The file must contain sets of named contaminants in the form name[tab]sequence. Lines prefixed with a hash will be ignored. |
Parameters in Workflow File
Type: fastqc
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| out-mode | Output directory | string |
| adapter | List of adapters | string |
| contaminants | List of contaminants | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Short reads
Name in Workflow File: in-file
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Source URL | url | string |