Cwltool uses docker --mounts

CWL Questions
1

I’m trying to implement tests for my cwl code in bitbucket pipelines. Therefore I need to run the cwl code using:

cwltool main.cwl inputs.yml

Although this works locally, if you run this in the bitbucket pipeline you get the following error:

docker: Error response from daemon: authorization denied by plugin pipelines: --mounts is not allowed.

I’ve tried the --udocker option but that would increase my run time considerably, which is why I would prefer another option.

Is there a way to avoid using the --mounts option to be able to run cwltool in the bitbucket pipeline?

2

Hello @tjvneste and welcome!

In cwltool, --mounts is required for use of docker. I’m surprised that bitbucket is allowing docker at all if they don’t allow --mounts, that is a very normal need for most users.

If you can satisfy the software dependencies another way, you can try running your workflow with cwltool --no-container.