Implement StepInputExpressionRequirements.

jmchilton commented 7 years ago

Needed by bcbio workflow and other GA4GH workflows.

http://www.commonwl.org/v1.0/Workflow.html#StepInputExpressionRequirement

[x] step-valuefrom-wf.cwl ./run_tests.sh -api test/api/test_cwl_conformance_v1_0.py:CwlConformanceTestCase.test_conformance_v1_0_61
[x] step-valuefrom2-wf.cwl ./run_tests.sh -api test/api/test_cwl_conformance_v1_0.py:CwlConformanceTestCase.test_conformance_v1_0_62
[ ] step-valuefrom3-wf.cwl ./run_tests.sh -api test/api/test_cwl_conformance_v1_0.py:CwlConformanceTestCase.test_conformance_v1_0_63

Will create a follow up issue on implementing over scattering - it looks like at least the BCBIO workflows do not require scattering and valueFrom on the same step. The vision chipseq workflows do require this however.

jmchilton commented 7 years ago

These tests require #55 first.

jmchilton commented 7 years ago

First crack is done at https://github.com/common-workflow-language/galaxy/pull/47/commits/4f4b5976c27340f431126f471c61332ba3ff00c9.

jmchilton commented 7 years ago

Got these first two test cases working - the third reveals some deep gaps between CWL and Galaxy - it seems steps can have inputs that don't match to tool inputs (I didn't know this) and that untyped inputs are essentially any inputs (which I did know but still is largely unimplemented).

jmchilton commented 7 years ago

https://github.com/common-workflow-language/galaxy/commit/4f4b5976c27340f431126f471c61332ba3ff00c9

and

https://github.com/common-workflow-language/galaxy/commit/7d8fcf22ef9de8874aee2a667e2fd08d406e9ca1

common-workflow-lab / galaxy

Implement StepInputExpressionRequirements. #52