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@leepc12 leepc12 released this 06 Oct 23:03
· 235 commits to master since this release
v1.4.0
a0579d9
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Learn about vigilant mode.

Change of CLI parameters:

  • --hide-subworkflow -> --show-subworkflow. Caper defaults to hide subworkflows.

Added features

  • --disable-auto-update-metadata: Disables auto write/update of metadata.json file on workflow's output root directory.
  • NBSubprocThread
    • Separated streaming (with two deamonized threads instead of one) of STDOUT and STDERR of a subprocess.
    • Better error handling. Correctly sends signal (signal.SIGTERM by default) to a subprocess thread when interrupted by stop().
  • CromwellRestAPI
    • find() defaults to exclude_subworkflow.
      • Does not retrieve all workflows unless wildcard (* or ?) is in a query as workflow_id or label (as value in a key/value pair).

Bug fixes

  • --java-heap-server not working
  • NBSubprocThread
    • Not correctly capturing Cromwell's STDOUT/returncode while gracefully dying.
  • Recursively sending too many requests to retrieve information of all workflows.
    • This recursively happened every update of workflow/subworkflow/task's status change, so lead to crash of Cromwell server running WDLs (e.g. ENCODE dnase-seq-pipeline) with nested subworkflows.
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