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Bump toil[cwl] from 5.6.0 to 5.8.0 #132

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@dependabot dependabot bot commented on behalf of github Jan 5, 2023

Bumps toil[cwl] from 5.6.0 to 5.8.0.

Release notes

Sourced from toil[cwl]'s releases.

5.8.0

No release notes provided.

5.7.1

Changelog

Highlighted Features Added

AWS Batch Batch System (#3956) AGC Integration (#4039) + More AGC integration (#4067) + AGC megabranch (#4113) Scale TES to be able to run reasonably-sized workflows on Funnel on Kubernetes with the AWS job store (#3927)

CWL

Run CWL conformance tests via WES (#4052) Implement and test CWL loadContents from URLs to fix #4125 (#4126) Add CWL tests under ARM (#4038) Cache results of cwltool version lookup (#4141)

Misc

SGE batch system change to support serial jobs. (#4022) Performance testing for Graviton instances (#4123) Stop waiting on hostpath volumes to exist (#4146) Catch and warn about jobs going away too slowly on FileJobStore (#4149) Add documentation for the type-checking hooks (#4117) Pod murder bot (#4060) Contrib hook scripts (#4105) Allow newer google-cloud-storage (#4114) Use environment variable to set parallel partition name (#4096) Register pytest markers (#4103) Mention --export=ALL for SLURM environments (#4100) (#4102) Allow persisting workflow state in WES server across container recreation (#4082) Change toil kill to use the job store shared file API to find pig.log (#4075) Bring back kill loop in the single_machine batch system but with a timeout (#4070) Reorganize Locking (#4059) Add and test preemptability constraints (#4044) Enhanced types (#3975) Use an init process that reaps zombies on toil clusters (#3974) Add launch cluster support for ARM (#3971) Feat: square bracket to period separator (#4008) Add AGC health check endpoint (#3997) Tolerate and require typed Werkzeug (#4011) Add more static URLs for Singularity debs (#4007)

Bug Fixes

Update WES set up docs (#4027) Add real time logs (#4031)

... (truncated)

Commits
  • 79792b7 Update version_template.py
  • 5f7218a Update flake8 requirement from <5,>=3.8.4 to >=3.8.4,<7 (#4304)
  • 4985938 Update networkx requirement from <2.8.8,>=2 to >=2,<2.8.9 (#4268)
  • a1e4a4c synchronize CLI options with argparse config (#4302)
  • 332eeed Allow determining of which jobs are running via toil status --replayBus (#4292)
  • 09c4a23 CWL: fix false warning when outputSource contains only one None value (#4...
  • 4c7ee3c Use pytest tmp_dir fixture for safe test paths (#4287)
  • af5e11f CWL: add --no-compute-checksum and a couple other missing options (#4291)
  • 88d4589 fileJobStore: handle arbitrary os.link errors to work on some filesystems (...
  • c894bbd Add prefix suffix params to getLocalTempFile (#4274)
  • Additional commits viewable in compare view

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Bumps [toil[cwl]](https://github.com/DataBiosphere/toil) from 5.6.0 to 5.8.0.
- [Release notes](https://github.com/DataBiosphere/toil/releases)
- [Commits](DataBiosphere/toil@releases/5.6.0...releases/5.8.0)

---
updated-dependencies:
- dependency-name: toil[cwl]
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added the dependencies Pull requests that update a dependency file label Jan 5, 2023
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dependabot bot commented on behalf of github Feb 6, 2023

Superseded by #133.

@dependabot dependabot bot closed this Feb 6, 2023
@dependabot dependabot bot deleted the dependabot/pip/toil-cwl--5.8.0 branch February 6, 2023 03:05
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