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).
Element type: write-assembly
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Data storage | Place to store workflow results: local file system or a database. | data-storage | string | |
| Document format | Document format of the output file. | bam | document-format | string |
| Build index (BAM only) | Build BAM index for the target BAM file. The file .bai will be created in the same directory. | True | build-index | boolean |
| Output file | Location of output data file. If this attribute is set, slot "Location" in port will not be used. | out-url | string | |
| Output file suffix | This suffix will be used for generating the output file name. | url-suffix | string | |
| 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 | write-mode | 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 |