DNAnexus OncoDEEP Upload

This is the DNAnexus implementation of oncodeep_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:

• file_to_upload - File to be uploaded (e.g. a Fastq file or Masterdata File)
• run_identifier - Identifier for the run, for example OKD1234. Specifies the subfolder name on the SFTP server
• account_type - Type of run (either 'Production' or 'Validation'). The type selected dictates the SFTP server that will be logged in to

Outputs

The following outputs are produced:

• logfile - For audit trail

How does this app work?

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

Developed by the Synnovis Genome Informatics Team