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2.0.0 release #382

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2.0.0 release #382

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@nebfield nebfield commented Oct 9, 2024 •
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Changelog

Improvements

  • Make report shareable by default
    • Remove individual level data
    • Don't show density plots with small sample sizes
  • Add warnings about complex alleles (e.g. HLA/APOE) and dosage specific effect weights to the report
  • The variant verification step added in 2.0.0-beta.3 has been integrated into pgscatalog-aggregate
    • The symmetric difference of scoring file variant IDs (.scorefile.gz) and variants that contributed to the final calculated score (.vars plink file) must be an empty set

Bug fixes

  • Stop crashing when encountering a scoring file with dosage specific effect weights (skip instead)
  • Fix report logo
  • Fix VCF input with JSON samplesheets
  • Add tar to zstd conda environment to prevent very old tar installs failing to extract the database
  • Reduce download max thread workers to prevent throttling by the EBI

Note

  • The COMBINE_SCOREFILES process may take longer to finish and use more memory than in previous versions
  • New internal variant data models were added in this release to improve handling complex alleles and dosage specific effect weights
    • Also, every variant (scoring file row) has many more validation steps now to ensure data quality and consistency
  • Speed and memory usage will be improved in the next release

@nebfield nebfield marked this pull request as ready for review October 9, 2024 13:33
@nebfield nebfield changed the title Integrate pgscatalog-utils 1.4.1 2.0.0 release Oct 10, 2024
@nebfield nebfield changed the base branch from dev to main October 10, 2024 12:27
This was linked to issues Oct 10, 2024
Make reports shareable by default #367
Open
Remove defaults channel from conda profile #366
Open
Improve PGS distribution plots in report for low sample numbers #345
Open
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@nebfield @smlmbrt