Dry run support in toil-wdl-runner

[unito-bot]

Julian wants to be able to dry-run a WDL workflow and “see all the commands that each task will actually execute (with the values filled in for variables)”. Then you could take the commands and document what commands a WDL workflow will run, as part of the workflow’s documentation.

He also suggested being able to turn the WDL task command blocks into plain Bash scripts in terms of variables.

┆Issue is synchronized with this Jira Story ┆Issue Number: TOIL-1582

[unito-bot]

➤ Adam Novak commented:

We might need to do some engineering in MiniWDL to make this work.

The hard part here is what to do about cases where the workflow structure depends on the actual results of container executions. Do you run some of the containers? How much symbolic fake execution would we need?

A workaround for not having this might be small test case inputs. We could try to improve how commands are logged to make it easier to collect the commands run form a Toil run.