Add --doubleTime argument

[adamnovak]

This should fix #5575.

While working on this, I figured out that chaining doesn't handle walltime correctly: it will chain to jobs for which there isn't enough walltime left.

I also was informed by somebody else's computer that, since the addition of walltime, the AbstractGridEngineBatchSystems that didn't have it added won't work anymore, since it gets passed around inside them anyway.

I'm not fixing any of that here, though. This should work for Slurm, and won't make chaining any worse.

Changelog Entry

To be copied to the draft changelog by merger:

• Toil now supports --doubleTime=True flag for increasing the walltime of failing jobs.
• Make Toil documentation suggest --defaultWalltime instead of --slurmTime.

Reviewer Checklist

• Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.
  • If it is coming from an external repo, make sure to pull it in for CI with:

    contrib/admin/test-pr otheruser theirbranchname issues/XXXX-fix-the-thing
    

  • If there is no associated issue, create one.
• Read through the code changes. Make sure that it doesn't have:
  • Addition of trailing whitespace.
  • New variable or member names in camelCase that want to be in snake_case.
  • New functions without type hints.
  • New functions or classes without informative docstrings.
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  • New or changed command line options for Toil workflows that are not reflected in docs/running/{cliOptions,cwl,wdl}.rst
  • New features without tests.
• Comment on the lines of code where problems exist with a review comment. You can shift-click the line numbers in the diff to select multiple lines.
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Merger Checklist

• Make sure the PR passed tests, including the Gitlab tests, for the most recent commit in its branch.
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• Copy its recommended changelog entry to the Draft Changelog.
• Append the issue number in parentheses to the changelog entry.

[adamnovak]

I have some more relevant synthetic code pushed up to general-walltime-improvements in my Toil fork, for trying to sort out the chaining.