For container based tools, I notice that I need to capture stdout/stderr as outputs.
For example, my tools fit this similar pattern:
cwlVersion: v1.2 class: CommandLineTool baseCommand: [echo] requirements: DockerRequirement: dockerPull: busybox id: "echo" inputs: message: type: string inputBinding: position: 1 outputs: echoOut: type: stdout
I notice that once a workflow finishes (in both cwltool and toil-cwl-runner), the outputs get written out in stdout. I am able to parse stdout of the workflow run to get the log files.
Is it possible to view logs in real time as a workflow runs? We are looking to support long running simulations and this is a requirement for our users.