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@DailyDreaming DailyDreaming released this 08 Jan 18:16
· 728 commits to master since this release
releases/5.2.0
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Learn about vigilant mode.

Changelog

CWL

  • Update to the latest cwltool (3.0.20201121085451 -> 3.0.20201203173111). #3375
  • Add better handling for potentially mis-ordered CWL args. #3395
  • Confirm CommandInputParameter expression can receive a File object. #3350

WDL

  • Make AnalyzeWDL abstract to allow implementation for different WDL versions #3391

Misc

  • Clean up memoize.py. #3374
  • Refactor bioio library, simplify logging, and small adjustments to utils. #3351
  • Use regular division for memory calculation on LSF. #3387
  • Remove unused --nodeOptions arg. #3397
  • Get boto S3 args for minio from environment variables. (#3370)
  • Update EC2 lists. #3376
  • Add a retry to AWS destroy. #3379
  • Regular division for memory calculation in LSF. #3387
  • Add option to blank mem allocation for SLURM. #3399
  • Preserve file permissions on imported/exported files #3322

Bug Fixes

  • Preserve file permissions on imported/exported files. #3322
  • Make building a flattened list of live jobs non-recursive. #3394
  • Move AWS job store uploads/downloads to boto3 (reopened) #3400
  • Use a Docker Hub mirror when pulling Docker images. #3411
  • Corrected gridengine maxMEM check to use memorystring #3410

Thank you to our contributors: @mr-c, @adamnovak, @w-gao, @jonathanxu18, @douglowe, @stevekm , @thiagogenez!

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