Sample metadata and files
Sample metadata and files¶
Gencove supports assigning metadata to a sample in JavaScript Object Notation (JSON) format.
Information commonly stored as sample metadata:
- phenotypes (characteristics) of the individual represented by the sample
- batch identifiers
- alternative or auxiliary sample identifiers
Each sample has many different files assigned to it that can be retrieved using the CLI.
The following CLI commands can be used to set and get metadata:
Assigning sample metadata¶
Metadata can be assigned to a sample using the gencove samples set-metadata command.
Specifying sample id and the --json flag together with a JSON string is mandatory.
Retrieving sample metadata¶
Sample metadata can be retrieved by using the gencove samples get-metadata
command. Optionally, --output-filename my-filename can be used to specify the filename
where the metadata will be output. If not specified, metadata will be printed to
stdout.
Downloading single sample file¶
Download and save file¶
A single sample file can be downloaded using the gencove samples download-file command.
Include checksum file¶
A single file can be downloaded along with its checksum file using the gencove samples download-file command.
Download and stream file to stdout¶
A single sample file can be downloaded and streamed to stdout using the gencove samples download-file command.