• Product manuals

Browse the manual

• Introduction
  • General information
  • Intended use statement
• User guide
  • Logging in to QCI Secondary Analysis Connector
  • Submitting samples for analysis
  • Monitoring sample analyses
    • Filtering sample analyses
    • Aborting analyses
    • Retrying failed analyses
    • Viewing analysis details
  • Submitting results to QCI Interpret
  • Downloading results
    • Configuring download settings
  • Managing secondary analysis workflows
  • Setting up automated sample submission
    • Starting and stopping automation
    • Configuring automation settings
  • Configuring proxy settings
  • Viewing product information
  • Viewing user manual
  • Contacting support
    • Saving logs
• System requirements
  • Linux and macOS
    • Support for checking if sequencing machine is done writing sample file to disk
  • Windows
    • Path length limit
• Appendix
  • Automation configuration concept definitions
    • Definition of sample completion
    • Definition of sample grouping
  • File browsers
  • Keyboard shortcuts

Definition of sample completion

Before the connector can submit a sample to a workflow, it has to know when the sample is complete, meaning that all sample files belonging to the sample have been completely written to the output folder of the sequencing machine. The connector supports two different methods for determining if a sample is complete:

• Trigger-file detection
• Files-per-sample detection

Trigger-file detection

Trigger-file detection is the preferred sample completion method, but it requires that the sequencing machine outputs a file to the output folder of the given sequencing run that signals that the sequencer is done writing all sample files to disk. The trigger-file must be located in the same folder tree as the sample files to submit for analysis.

The benefits of trigger-file detection are:

• The connector does not have to check each individual file to see if it has been completely written to disk. This check requires that the operating system is able to determine if a file is currently being written to, and this is not supported in certain scenarios.
• It is not necessary to set a specific number of files per sample produced by the sequencing machine. The sequencer can thus be reconfigured to produce a different number of files per sample without also having to update the workflow's automation configuration.

If the sequencing machine does not produce a file that is consistently created after all sample files have been written to disk, it is possible to use a different file created by the sequencer and adding a delay between when the file is detected and when the connector should start searching for related sample files (see Sample completion setting).

Files-per-sample detection

If the sequencing machine does not support trigger-file detection, the fallback method is defining how many files the sequencer produces per sample. Caution should be taken when using this method. If the sequencer is reconfigured to produce a different number of files per sample, the workflow's automation configuration has to be updated accordingly before a new sequencing run is started.

If files-per-sample detection is used, the operating system must be able to determine if a file is currently being written to. See System requirements for information about platform specific system requirements.

---