V-Pipe Integration
Utilities for working with V-Pipe output and file naming conventions.
Sample
sr2silo.vpipe.Sample
A sample object for V-Pipe.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
sample_id
|
str
|
The sample ID. |
required |
organism
|
str
|
The organism identifier (e.g., 'covid', 'rsva'). Optional, defaults to 'covid' for backward compatibility. |
'covid'
|
config_path
|
Path | None
|
Optional path to an external timeline columns YAML file. If provided, used instead of the bundled one. |
None
|
enrich_metadata(timeline)
Enrich the sample metadata with additional information.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
timeline
|
Path
|
The path to the timeline file. |
required |
get_metadata()
Get the metadata for the sample.
set_metadata()
Get the metadata for the sample.