Getting started
Start by logging in to the QCI Secondary Analysis Connector as described in Logging in to QCI Secondary Analysis Connector.
Configure one or more cloud accounts (AWS), as described in Cloud accounts, if sample files are to be imported from, or analysis results exported to, cloud storage.
Before submitting samples for secondary analysis, the secondary analysis workflow(s) must be activated as described in Managing secondary analysis workflows, and the following settings (available in the settings menu in the top right of the connector) should be configured as needed:
- Status file settings: The connector can write a JSON formatted file to disk or cloud storage containing the status of submitted analyses. The file is updated with new information on a regular basis. The file can be parsed by internal systems that need information about the submitted analyses. See Status file settings for additional information.
- Upload settings (see Upload settings):
- Maximum number of concurrent uploads: The maximum number of sample files to upload in parallel.
- Download settings (see Download settings):
- Download location: The location to which results should be downloaded.
- File extension filter: A filter that can be enabled to control which secondary analysis result types to download.
- Download completion file: A setting that can be enabled to create a file in the results folder for a given analysis when download of results has completed. The presence of this file can be used by internal systems to trigger downstream processes.
- Maximum number of concurrent downloads: The maximum number of result files to download in parallel.
- Cloud export settings (see Cloud export settings):
- Cloud export location: The location to which results should be exported.
- File extension filter: A filter that can be enabled to control which secondary analysis result types to export.
- Cloud export completion file: A setting that can be enabled to create a file in the results folder for a given analysis when export of results has completed. The presence of this file can be used by internal systems to trigger downstream processes.
Submit sample files for secondary analysis either manually or automatically by following Submitting samples for analysis or Setting up automated sample submission, respectively.
Monitor the submitted samples as described in Monitoring sample analyses.
If any of the following result actions were not requested during sample submission, they can be performed manually after the analysis completes as described in the referenced sections:
- Submission of results to QCI Interpret for variant interpretation (see Submitting results to QCI Interpret).
- Download of results (see Downloading results).
- Export of results to cloud storage (see Exporting results to cloud storage).