Version

Pipeline Version

1.4.1

Software Dependencies

Specific versions used in your run are automatically captured in the software_versions.yml.

Platform Information

Deeplex Myc-TB

v1.4.1

  • Added sample-to-patient UUID mapping so Deeplex sample IDs can be pre-associated.

  • Added a standalone OAuth token helper script: scripts/get_access_token.py.

  • Move the log.info to inside the workflow.

  • Docker image and support

v1.4.0

  • Removed VCF processing, lineage analysis, and sample report generation.

  • Fixed UPLOAD_FHIR process to FHIR transaction bundles.

  • Removed VCF-related parameters (vcf_dir, reference, repetitive_regions, lineage_barcode, clinical_metadata).

  • Add custom LOINC code for specific Deeplex codon change (replacing gHGVS).

References

  1. Di Tommaso, P., et al. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology.

  2. Genomics Reporting Implementation Guide v3.0.0. Variant Reporting