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Nanostream management application

Nanostream management application is designed to run/stop previously deployed dataflow templates.

You can deploy the application to your project using install script. You can access deployed application by url: https://<your project id>.appspot.com

New Pipeline screen

To create and run a new pipeline fill form fields:

  • Pipeline Name - an arbitrary name to identify your pipeline.
  • Input Folder - a folder in your upload bucket, a place for your input data.
  • Pipeline Type - select appropriate value: "species" or "resistance_genes".
  • Auto-stop - number of seconds no new files added to the pipeline to stop.
  • Auto-start checkbox - pipeline starts if a data uploaded to Input Folder.
  • Start immediately checkbox - start pipeline right after START button pressed.
  • Reference databases block:
    • database name - a name to identify your database;
    • reference database uri - path to your FASTA file like: gs://<your project id>-reference-db/db1/DB_viruses_12345678.fasta;
    • taxonomy file uri - path to your taxonomy file like: gs://<your project id>-reference-db/taxonomy/species_tree.txt

Available Pipelines list screen

Contains list created pipelines. Consists of a table with columns:

  • Name - pipeline name
  • Input folder - your pipeline input folder
  • Output collection name prefix - Firestore collection prefix to output results
  • Processing mode - pipeline processing mode
  • Input data subscription - a link to corresponding GCP subscription bounded to pipeline
  • Jobs - list GCP dataflow jobs
  • Created at - when pipeline was created
  • Status - current pipeline status
  • Autostart - a checkbox to set pipeline autostart property
  • Remove - a button to remove pipeline (just remove pipeline info created at "New Pipeline" screen; no uploaded data removed)

Available Jobs list screen

Contains list CGP dataflow jobs. Columns:

  • Name - job name
  • Start time - when job started
  • Stop time - when job stopped (for not running jobs)
  • Current state - job state
  • Stop - a button to cancel job

Pipeline details screen

Contains reference to pipeline info.

When some data saved to Firestore database you can see them on a chart or a table: Chart Table

Each input data folder corresponds a result file in a Firestore collection. You can choose it in a dropdown.