Bump toil[cwl] from 4.1.0 to 5.4.0

[dependabot[bot]]

Bumps toil[cwl] from 4.1.0 to 5.4.0.

Release notes

Sourced from toil[cwl]'s releases.

5.4.0

No release notes provided.

5.3.0

No release notes provided.

5.2.0

Changelog

CWL

• Update to the latest cwltool (3.0.20201121085451 -> 3.0.20201203173111). #3375
• Add better handling for potentially mis-ordered CWL args. #3395
• Confirm CommandInputParameter expression can receive a File object. #3350

WDL

• Make AnalyzeWDL abstract to allow implementation for different WDL versions #3391

Misc

• Clean up memoize.py. #3374
• Refactor bioio library, simplify logging, and small adjustments to utils. #3351
• Use regular division for memory calculation on LSF. #3387
• Remove unused --nodeOptions arg. #3397
• Get boto S3 args for minio from environment variables. (#3370)
• Update EC2 lists. #3376
• Add a retry to AWS destroy. #3379
• Regular division for memory calculation in LSF. #3387
• Add option to blank mem allocation for SLURM. #3399
• Preserve file permissions on imported/exported files #3322

Bug Fixes

• Preserve file permissions on imported/exported files. #3322
• Make building a flattened list of live jobs non-recursive. #3394
• Move AWS job store uploads/downloads to boto3 (reopened) #3400
• Use a Docker Hub mirror when pulling Docker images. #3411
• Corrected gridengine maxMEM check to use memorystring #3410

Thank you to our contributors: @​mr-c, @​adamnovak, @​w-gao, @​jonathanxu18, @​douglowe, @​stevekm , @​thiagogenez!

5.1.0

Version 5.1.0

Changelog

WDL

• Add WDL cross function. #3360

Bug Fixes

• Better error message for insufficient disk. #3362
• Fix maxMEM comparison in LSF. #3369

... (truncated)

Commits

• 87293d6 Update version_template.py
• e5b6261 Update AWS instance list. (#3673)
• 73dfafa Update PULL_REQUEST_TEMPLATE.md
• 6d00bf8 Add type hints to toilLaunchCluster.py (#3656)
• 2c6a779 Override size function for ToilFsAccess (#3670)
• 4f99fe8 Add type hints to abstractJobStore.py (#3659)
• 32e73d5 Better explain where to write the changelog entry (#3671)
• fd805d5 Set encoding to string in tutorials (#3668)
• 6b882c6 Add type hints (#3657)
• 5a1f4c0 Add type hints (#3647)
• Additional commits viewable in compare view

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[dependabot[bot]]

Looks like toil[cwl] is up-to-date now, so this is no longer needed.