Arvados

18994-cwl-basename @ bf95fa077c79c6bd4ac548ec534b618e97e3f00b

• Added integration test for this case
• Now includes check for "basename" in check whether input files need to be re-staged into a new intermediate collection
• The actual re-staging already uses basename correctly

developer-run-tests: #3056

18994-cwl-basename @ 5d039c344850dfc5fedd03c1050fa51eec404d72

• Fix tests
• Better handling of optional dependencies
• Bonus fix for #18614
• passed CWL conformance tests on arvbox
• passed Arvados CWL integration tests on arvbox

developer-run-tests: #3066

re-run: developer-run-tests-apps-workbench-integration: #3275

re-run: developer-run-tests-apps-workbench-integration: #3276

Just one observation:

• In runner.py there're a number of commented out code lines left.

The rest LGTM