Definition of sample completion

Before the plugin can submit a sample to an analysis 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 sequencer's output folder. The plugin supports two different methods for determining if a sample is complete:


Trigger-file detection

Trigger-file detection is the preferred sample completion method, but it requires that the sequencer 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 a folder belonging to the same folder tree as the sample files (see example in figure 4.6).

The benefits of trigger-file detection are:

If the sequencer 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 plugin should start searching for related sample files (see Sample detection delay).


Files-per-sample detection

If the sequencer 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 Analysis Automation Server Plugin configurations have 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.