Upgraded version of cwltool to 3

[zagganas]

Upgraded the version of cwltool to support CWL 1.2 and made relevant changes.

[kellrott]

Looks like after the most recent merge of 0.4.0 branch, you'll need to re-do the requirements. The minio client isn't installed.

[kellrott]

It looks like that between versions of CWL, the order of the tests was changed. The line https://github.com/ohsu-comp-bio/cwl-tes/blob/master/tests/test_conformance.py#L24 needs to be updated to skip the test with writable outputs. We'll have to address that issue, as that requirement is not currently supported by TES ( https://github.com/ga4gh/task-execution-schemas/issues/18 )

[mr-c]

It looks like that between versions of CWL, the order of the tests was changed. The line https://github.com/ohsu-comp-bio/cwl-tes/blob/master/tests/test_conformance.py#L24 needs to be updated to skip the test with writable outputs. We'll have to address that issue, as that requirement is not currently supported by TES ( ga4gh/task-execution-schemas#18 )

You can now skip tests by name, instead of number: https://github.com/common-workflow-language/common-workflow-language/blob/efe30c092a29924ebe00f7a0edf3a413a9bdb1a7/run_test.sh#L17