Update cwltool requirement from ==3.1.* to >=3.1,<3.3

[dependabot]

Updates the requirements on cwltool to permit the latest version.

Release notes

Sourced from cwltool's releases.

3.2.20260411152607

What's Changed

• cwl_utils 0.41 by @​mr-c in common-workflow-language/cwltool#2225
• pin pygments by @​mr-c in common-workflow-language/cwltool#2226
• [Snyk] Fix for 4 vulnerabilities by @​mr-c in common-workflow-language/cwltool#2227
• Fix all_non_null single source element by @​LanderOtto in common-workflow-language/cwltool#2220

Deps

• build(deps-dev): update setuptools-scm requirement from <10,>=8.0.4 to >=8.0.4,<11 by @​dependabot[bot] in common-workflow-language/cwltool#2222
• build(deps): bump codecov/codecov-action from 5 to 6 by @​dependabot[bot] in common-workflow-language/cwltool#2223
• build(deps): update galaxy-tool-util requirement from !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<25.2,>=22.1.2 to >=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<26.1 by @​dependabot[bot] in common-workflow-language/cwltool#2229

Full Changelog: common-workflow-language/cwltool@3.1.20260315121657...3.2.20260411152607

Commits

• 55223a6 Fix all_non_null single source element (#2220)
• 99516ea fix: requirements.txt to reduce vulnerabilities
• 4999410 build(deps): update galaxy-util requirement from <25.2 to <26.1
• a215f69 build(deps): update galaxy-tool-util requirement
• 45e660e shellcheck cleanup
• ca173ba tox: match the python version used by GitHub Actions
• 47a6006 pin minimum pygments version to avoid CVE-2026-4539
• ff0e409 upgrade to cwl_utils 0.41 and use the new types
• 99cac79 build(deps): bump mypy from 1.19.1 to 1.20.0
• 8b55ebc build(deps): bump codecov/codecov-action from 5 to 6
• Additional commits viewable in compare view

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