6.1.0

Highlighted Features Added

• WDL and CWL task standard output and standard error logs that are not captured by the workflow will now be logged at INFO level and stored in the --writeLogs/--writeLogsGzip directory. (#4657)
• Use a default log limit of 100MiB (#4788)

Breaking Changes

• Stats and logging system again uses job display name (#4755)
• --disableProgress is once again a flag that doesn't take an argument (#4758)

CWL

• Don't clear out user-provided values for the --default-container option (#4730)

WDL

• WDL job names now include numbers for scatters (#4755)
• Multi-line WDL placeholder substitutions no longer interfere with de-indenting WDL command blocks (chanzuckerberg/miniwdl#665)
• Standard error for failed tasks is now always logged to the worker log somewhere (#4781)

Kubernetes

Dependencies

• Deps: removed the ruaml.yaml.string plugin dependency for a simpler solution (#4760)

Misc

• Toil will no longer warn about a missing XDG_RUNTIME_DIR (#4769)
• Read the Docs and CI docs builds should have Graphviz installed (pending CI image rebuild) (#4734)
• Add more Python3.12 compatibility by replacing the one function from distutils that we use, strtobool(). (#4765)
• Set default cache folders to be accessible between toil-wdl-runner workflows (Same as MiniWDL/Singularity defaults) (#4761)
• Set toil-wdl-runner cache folders on Toil managed clusters to be at /var/lib/toil (#4761)
• Fall back to assuming machine has 1 core when CPU count is unavailable. (#4545)
• FileJobStore now supports filenames that get modified when percent-encoded (#4779)

Thank you to our contributors:

@DailyDreaming @mr-c @stxue1 @adamnovak @app/dependabot

Full Changelog: releases/6.0.0...releases/6.1.0