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Oncogenomics_NF_WF 5.5.0

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@vinegang vinegang released this 23 Jul 14:58
5.5
13fe5f1
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🚀 Release highlights
This release includes unification of AWS healthomics and biowulf pipeline versions.

✨New Features

  • Unified Workflow Completion Tracking

    • Refactored creation of successful.txt to be process-based instead of Groovy script for proper pipeline completion on healthomics.
    • Introduce Allstepscomplete process to all the workflows (Exome, Tumor-Normal, RNA-seq, RNA-seq multi-lib).
    • Add a global ch_allcomplete channel to capture outputs from key processes and signal workflow completion.
    • Generate a successful.txt marker file upon completion for downstream tracking (e.g., AWS Step Functions integration).

  • New Configuration Options

    • Add support for hg38 with a dedicated configuration file. - In progress
    • Update AWS-specific config (aws_nextflow.config) and renamed local cluster config to biowulf_nextflow.config for clarity.

  • Enhanced Compatibility

    • Add a conditional check to prevent FusionCatcher failures when no fusions are detected.
    • Remove the trap command from the OptiType process to avoid HealthOmics execution errors.

🛠️ Improvements

  • Output Standardization

    • Update output tuple formats across multiple processes for better compatibility.
    • Capture meta information into the output config file for easier downstream parsing.

  • Docker and Tool Updates

    • Update Strelka Docker image to the latest compatible version.
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