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
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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 |
boolean
string
Type: write-assembly
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 |