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Workflow Basics

AstraKit: Workflow Basics AstraKit provides automated workflows for precision medicine, including variant annotation and filtering, multi-omics data analysis, cohort analysis of molecular profiles, and drug screen analysis. Please note that the workflows require Python and R, which must already be installed on the host system. The associated KNIME extensions can be installed automatically in KNIME. To create a workflow, add a reader node in your data format. Processed data can be written out again using a writer node.
Reader nodes To select a file to load, right-click on the reader node and click on 'Configure'. To select a local file, choose 'Local file system' at 'Read from'. Check in the window below whether the data has been loaded correctly. You may need to adjust the column or row separator, or the column headers.
Writer nodesSimilarly, you can select an output file by right-clicking > Configure.
Annotation
Filtering
Reader nodes
Writer nodes
Variant annotation and filtering To interpret genetic variant data, add a reader node in your variant data's format (VCF, MAF, CSV), followed by a '_to_BFrame' node in the variant data's reference genome. To get a full overview of all possible nodes, open the workflow '00 - Node Overview'.
Set up Python environmentFor workflows using Python nodes, you need to have Python >3.9 installed on your device. After installing the Python interpreter, AstraKit can automatically install the required Python packages, if you link a ‘Set up Python env’ node at the beginning of your workflow to another Python node. To do this, create a flow variable link by dragging the mouse between the upper corners of the Python nodes (incated by a red line).
Connecting nodesYou can link nodes that have the same input and output format, e.g. an arrow for a table or a blue rectangle for an object.
VCF-Reader
File Reader
Set up python env
Python Script
BFrameto_VCF
Python Script
Processing
Python Script
VCF-WriterVariants
CSV Writer
Definefilteringoption
Variable Creator
Pathogenicityscores
Python Script
Proteinannotation
Python Script
Processing
Python Script
Filter ClinVar
Python Script
VCF Writer
CSV Writer
Processing
Python Script
Proteinannotation
Python Script
VCF_to_BFrame (GRCh37)
Python Script
VCF_to_BFrame (GRCh37)
Python Script
VCF-Reader
File Reader

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: nsk
Created at: 2025-10-23
On NodePit since: 2025-10-27
Last update: 2025-10-30
Created with KNIME version: v5.8.0

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