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Oncogenomics_NF_WF 5.4.0

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@vinegang vinegang released this 06 May 15:22
5.4.0
4548031
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🚀 Release Highlights
This release includes several new features, improvements, and bug fixes focused on enhancing CNV annotation, handling complex inputs, improving AWS integration, and better parameter parsing.

✨ New Features

  • CNVKit Enhancements

    • Introduce cnvkit_annotation process and supporting Python script.
    • Add Docker image and cluster resources for cnvkit_annotation.
    • Update cnvkitpaired process to consume outputs from Mutect and Sequenza.

  • Mutational Signature Logic

    • Conditionally run mutational signature analysis only when mutation count > 50.

  • RNA and Sample Metadata Handling

    • Improve support for multiple RNA libraries tied to the same tumor library.
    • Enhance handling of comma-separated lists in sample inputs.
    • Extracte and pass patientID and casename to AWS utility functions.

  • Mutation Burden Support

    • Add mutation burden reference for seqcapez.rms.v1 kit.
    • Integrate mutation burden calculation logic for this kit.

🛠 Improvements

  • Refactor onComplete block and Groovy functions to use patientID and casename instead of nextlfow workflow parameters.(As these cannot be used on healthomics)
  • Include updated publishDir logic to ensure FastQC results appear under the results/ folder.
  • Remove sh from shell scripts that caused compatibility issues on AWS healthomics

🐞 Bug Fixes

  • FusionCatcher - Include graceful exit when FusionCatcher returns no results, avoiding unnecessary failures.
  • SampleSheet Parsing - Improve logic to robustly extract patientID and casename even with comma-separated entries.
  • Add Platform as a configurable parameter.
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