Bug #13252
Updated by Jiayong Li about 6 years ago
I'm trying to run a workflow in a single container but it failed. https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-8d7o1hq6mnnri85
I've got the following error.
<pre>
2018-03-21T00:06:23.256283830Z [step eagle] start
2018-03-21T00:06:23.260142930Z Exception on step 'eagle'
2018-03-21T00:06:23.260701530Z Cannot make scatter job: --no-container, but this CommandLineTool has DockerRequirement under 'requirements'.
2018-03-21T00:06:23.261063530Z Workflow cannot make any more progress.
2018-03-21T00:06:23.261720930Z Final process status is permanentFail
</pre>
However, the script eagle.cwl does NOT have DockerRequirement.
See the attached tar ball for the cwl scripts. The command I was using:
<pre>
arvados-cwl-runner --api=containers --submit --no-wait --project-uuid su92l-j7d0g-huzwo8ptw745hjx phasing-wf.cwl yml/phasing-GS12877.yml
</pre>
Note that without the RunInSingleContainer requirement, the workflow completed. https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-94180nzfj7yz6q5
For the record
<pre>
arvados-cwl-runner --version
/usr/bin/arvados-cwl-runner 1.0.20180223182850, arvados-python-client 0.1.20180223161544, cwltool 1.0.20180130110340
</pre>