DNAnexus Qiagen Upload

This is the DNAnexus implementation of qiagen_upload v1.0.0. For further details on what the underlying script does and produces, please refer to that repository.

Inputs

The app takes the following inputs:

• sample_name - Name of TSO sample to be uploaded
• sample_zip_folder - sample_zip_folder

If a sample_zip_folder and sample_name is provided, the app will run in upload mode and will upload the sample to QCII.

If no sample_zip_folder and sample_name is provided, the app will run in user code generation mode, and will generate the keys required to register the device in QiaOAuth.

Outputs

If the app runs in upload mode, the following outputs are produced:

• sample_xml - XML file created that was added to the zip folder for sample upload (XML file is required by Qiagen as part of the upload)
• logfile - for audit trail

If the app runs in user code generation mode, the following outputs are produced:

• code_verifier_file - Text file containing code_verifier key
• device_code_file - Text file containing device_code key
• user_code_file - Text file containing user_code key
• Logfile - for audit trail

Device Registration

For this app to function, the device must have an active registration in QIAGEN Digital Insights OAuth2 Server. For instructions on how to do this / keep this updated, please refer to KB0010624.

How does this app work?

• This app runs a python scripts located inside a docker image.

Developed by the Synnovis Genome Informatics Team