The element gets message(s) with assembled reads data and saves the data to the specified file(s) in one of the appropriate formats (SAM, BAM, or UGENEDB).
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Data storage | Place to store workflow results: local file system or a database. | |
| Document format | Document format of the output file. | bam |
| Build index (BAM only) | Build BAM index for the target BAM file. The file .bai will be created in the same directory. | True |
| Output file | Location of output data file. If this attribute is set, slot "Location" in port will not be used. | |
| Output file suffix | This suffix will be used for generating the output file name. | |
| Existing file | If a target file already exists, you can specify how it should be handled: either overwritten, renamed or appended (if supported by file format). If Rename option is chosen existing file will be renamed. | Rename |
Parameters in Workflow File
Type: write-assembly
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| data-storage | Data storage | string |
| document-format | Document format | string |
| build-index | Build index (BAM only) | boolean |
| out-url | Output file | string |
| url-suffix | Output file suffix | string |
| write-mode | Existing file | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: Assembly
Name in Workflow File: in-assembly
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Assembly data | assembly | assembly |
| Location | url | string |