Bump toil[cwl] from 4.1.0 to 5.0.0

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Bumps toil[cwl] from 4.1.0 to 5.0.0.

Release notes

Sourced from toil[cwl]'s releases.

5.0.0

Caching is now turned on by default.

CWL v1.1 is also now fully supported and passing all conformance tests.

The following batch system names are now deprecated (#3225) and replaced by:

• singleMachine -> single_machine
• gridEngine -> grid_engine
• LSF -> lsf
• Mesos -> mesos
• Slurm -> slurm
• Torque -> torque
• HTCondor -> htcondor
• Kubernetes -> kubernetes
• k8s -> kubernetes

Changelog

CWL

• Upgrade to a CWL v1.2.0 capable cwltool (3.0.20200709181526 -> 3.0.20200807132242). #3137
• Export to a bucket if cwl's CreateFile is specified. #3124
• CWL v1.1 Support: loadContents if True for StepValueFrom objects. #3266
• CWL: Fix workdir permissions. #3229
• Test CWL secondary file from s3. #3311
• CWL v1.1 Support: Inplace update has side effect on directory content. #3280
• More CWL v1.2 conformance tests. #3336
• CWL: Reformat w/ Black and better support for tmpdir_prefix with suffix. #3333

WDL

• Add ceil() and floor() WDL functions. #3168
• Create a stdout and stderr file for each WDL task. #3181
• Add WDL write functions and builtin tests. #3236
  • write_lines
  • write_tsv
  • write_json
  • write_map
• Add WDL read functions and builtin tests. #3244
  • read_lines
  • read_tsv
  • read_json
  • read_map
  • read_int
  • read_string
  • read_float
  • read_boolean
• Add transpose() WDL function. #3273
• Add length() WDL function. #3307
• Add sub() WDL function. #3252
• Add range() WDL function. #3277
• Add size() WDL function. #3255

Commits

• f182c64 Update version_template.py
• 3df0204 CWL Test #307: Confirm CommandInputParameter expression can receive a File ob...
• 2ed5f3c Add WDL zip() function + tests. (#3355)
• 3a8663a Replace abssympath with a builtin. Add test. (#3356)
• 3d06051 LSF: handle unicode configuration files (#3354)
• 40d5ecc Remove unused lib items. (#3347)
• 3f03dec Refactor WDL types (#3335)
• 3b1f756 Only rm a statefile that exists. (#3348)
• e7d0908 getting job details from scontrol is now functional. (#3346)
• 192151d Update cactus commit to test latest. (#3342)
• Additional commits viewable in compare view

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[dependabot-preview[bot]]

A newer version of toil[cwl] exists, but since this PR has been edited by someone other than Dependabot I haven't updated it. You'll get a PR for the updated version as normal once this PR is merged.

[dependabot-preview[bot]]

OK, I won't notify you again about this release, but will get in touch when a new version is available.

If you change your mind, just re-open this PR and I'll resolve any conflicts on it.