Batch Metadata Injection is a SeqWare plugin that allow you to inject basic metadata for a sequencer run, study, and other associated information. It has several mechanisms available to insert these data. In the default mode, fields specified on the command line and other information provided in a file allow you to create the metadata without prompting. Alternatively, you can use interactive mode to be prompted for each step in creating the metadata, which may occur with or without an input file..
The plugin was originally developed to import metadata needed to process data that originated outside of, or could not be entered into, the LIMs system at OICR. Therefore, it mimics the process of a sequencer run being entered into the LIMs and the import process necessary in the SeqWare MetaDB. The system uses the name as a unique identifier for Study and Experiment, allowing you to add additional samples to a pre-existing Study. Every sequencer run is considered to be unique though.
Information is collected first and stored in-memory before attempting to create the objects in the database, so you may exit the process at any time prior to database insertion without causing any database corruption.
Sequencer Run - this element descibes the flowcell or single run of a sequencer.
Lane - this element describes a lane of sequencing in the flowcell. It may contain one or more samples or barcoded samples in the form of IUSes (below). It is unique to a Sequencer Run.
IUS - short for Individual Unit of Sequencing, this element describes a sample loaded in a lane, or a barcoded sample in a lane. It is unique to a Lane and Sequencer Run.
Study - this element contains the information about the project that the samples belong to. This element can contain many samples from different lanes of sequencing.
Experiment - this element can be used to distinguish different types of experiments within a project, for example samples that relate to WG or exome sequencing.
Sample - this element describes a particular library used for sequencing. The exact name of the sample is created with the attributes specified at run time.
In order to run the WorkflowRunReporter plugin, you must have the following available to you:
|–miseq-sample-sheet||Optional: The absolute or relative path to the sample sheet. Use instead of –new|
|–interactive||Enable interactive mode|
|–new||Optional: Create a new sequencer run and study. Use instead of –miseq-sample-sheet|
Here a number of examples of how to use the plugin.
java -jar $SEQWARE_HOME/seqware-distribution-1.0.0-full.jar --plugin net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection -- --new --interactive