Data Processing

Main Workflow

File: main.nf The main workflow handles channel processing and parallel execution.

Deeplex Excel Report Workflow

File: deeplex.nf For processing Deeplex Myc-TB output files (Excel format)

  1. Conversion:

    • Script: xlsx_json_converter.py

    • Function: Parses Excel sheets (‘Drug resistance variants’, ‘Uncharacterised variants’, ‘Phylo_Syn variants’) to extract variant and lineage data.

    • Mapping: Maps drugs to SNOMED CT and variants, lineage to LOINC.

  2. Clinical Data Merge:

    • Script: merge_clinical_deeplex.py

    • Function: Aggregates observations to DiagnosticReport.

    • Resistance Classification: Classifies samples (e.g., MDR-TB, XDR-TB) based on detected drug resistance profiles.

    • Patient UUID integration: Integrate patient UUID to the FHIR Bundles.

Upload to FHIR Server

File: upload_fhir.nf For uploading FHIR Genomics bundle with linked patient UUID. Must grant bearer token first using scripts/get_access_token.py.

Workflow Parameter

nextflow.config defines all input files, directories, versioning, and specific tool parameters, relative to the base directory ($baseDir).