How to launch the DRAGEN COVID Lineage app using BaseSpace CLI?

The DRAGEN COVID Lineage app supports the use of individual Biosamples or entire projects as input. BaseSpace Command Line Interface (CLI) can be used to launch the app as shown below.

Example of launching DRAGEN COVID Lineage with a project as input in a professional workgroup:

bs launch application -n 'DRAGEN COVID Lineage' --app-version 3.5.9 -o project-id:<Output Project ID> -o basespace-labs-disclaimer:Accepted -o input-project-id:<Input Project ID> -o input-type:project -o virus-primers:ncov2019 -c workgroupname  

Example of launching DRAGEN COVID Lineage with Biosamples as input in a professional workgroup:

bs launch application -n 'DRAGEN COVID Lineage' --app-version 3.5.9 -o project-id:<Output Project ID> -o basespace-labs-disclaimer:Accepted -o sample-id:<Biosample IDs separared by commas> -o virus-primers:ncov2019 -c workgroupname  

To see the list of application options in csv format:

bs  launch application -n "DRAGEN COVID Lineage" --list  -f csv  

Note

• The license agreement associated with this application must be signed by a user before launching using BaseSpace CLI. To do so, navigate to the application launch page, scroll to the bottom, select the EULA, and accept the license agreement.

  
• Users can run this command to load BaseSpace credentials into the environment: 'eval $(bs config load config_name)'. Subsequently, the -c flag no longer needs to be included in launch commands.

• When selecting an Input Project, a maximum of 1536 samples is supported.

  • If a project contains more than 1536 samples, the app may appear to launch, but it will quickly terminate.

  • It is strongly suggested to use 1 project per flow cell/sequencing run.

• When selecting Input Samples: The app will launch reliably with 60 samples or fewer.

  • When analyzing a larger number of samples, break them up into groups of 60, or use the Input Project to select an entire project.

• A virus primer BED file must be selected while launching the app. Currently available options are none (for library types such as enrichment), ncov2019 (ARTIC v3 primer BED), articv4 (ARTIC v4 primer BED), articv4.1 (ARTIC v4.1 primer BED), or custom.

  • Note that a custom primer BED must be in the format of an ARTIC Primer Scheme as well. For further information, search for Knowledge Base article How can a custom virus primers BED file be used with the DRAGEN COVID Lineage app on BaseSpace?

For any feedback or questions regarding this article (Illumina Knowledge Article #5230), contact Illumina Technical Support [email protected].