Bump toil[cwl] from 5.6.0 to 5.8.0

[dependabot]

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

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

[dependabot]

Superseded by #133.