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@vasimuddin vasimuddin released this 08 Apr 16:17
· 50 commits to main since this release
2.1
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v2.1 release updates and adds fixes to AlphaFold2 pipeline and DeepVariant-based germline fq2vcf pipeline.

  • AlphaFold2-based protein folding pipeline:

    • Enabled inference using different models
    • Bug fixes for running Model 3, 4, & 5.
    • Removed unnecessary paths from run script.
    • Enabled use of contiguous tensor inside TPP PyTorch extension

  • DeepVariant-based germline variant calling (fq2vcf) pipeline :

    • Enabled support for gzipped reference sequence file as input
    • Enabled support for reads and reference sequence data files to be in different folders
    • Enabled cleanup of all intermediate data generated during the pipeline's run
    • Provided an option to keep the intermediate SAM files out of bwa-mem2
    • Fixed the messaging to the user in case of a failed run
    • Updated README with precise instructions to run on various types of compute environments
    • In AWS parallel cluster environment: enabled index creation on a compute node instead of the master node
    • Added details in README about memory and disk requirements for a run using a Human WGS dataset
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