Arvados

Review comments:

1. I created a workflow using the following command:

130!radhika@shell.9tee4:~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --create-workflow bwa-mem.cwl bwa-mem-input.yml
/usr/bin/arvados-cwl-runner 0fb93082a34a92699c9be9ed4b1c991dd4003ea1 1.0.20161206185818, arvados-python-client 0.1.20161128194626, cwltool 1.0.20161128202906
Resolved 'bwa-mem.cwl' to 'file:///home/radhika/arvados/doc/user/cwl/bwa-mem/bwa-mem.cwl'
9tee4-7fd4e-i436kksnp4upnb8

I then went to 9tee4 workbench and used "Run a process" and selected this workflow. The resulting CR, 9tee4-xvhdp-fkm20ytkjp9g189, has the inputs filled in as expected.

However, the CR run failed with "Unsupported scheme in url: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_1.fastq"

• Create a workflow with a cwl and partial input or a fixture in this state
• Run a process using this workflow
• Verify that the provided partial inputs are filled and the others are empty

For comment (1) this requires the fix in #10576.

For (2), I will see about adding a test.

I extended the test that creates a new pipeline/workflow to check that the parameter with a default value is filled in.

Now at @ 08271aa69aafdc92e2e8f8f25ed7fab078deb993

It would be nice to also add one more assertion to the test(s) that the Run button is disabled, since at least one required parameter is empty.

LGTM

Thanks.