Description
Expected Behavior
I would expect that I should be able to look at a workflow and see all the input files that it requires.
i.e. cwltool should warn/reject workflows that define additional inputs buried in tools as opposed to the "root" workflow
Actual Behavior
It seems that secondary files can be defined at the tool level and cwltool picks them up "properly" meaning that someone using a workflow will need to review both the workflow and all imported tools in order to get a complete picture as to what input is required.
(Unfortunately, addressing this seems to be a breaking change. Note that the ticket this was originally raised in was common-workflow-language/common-workflow-language#362 )
Workflow Code
https://gist.github.com/denis-yuen/730b3504732bcb26f65bd2e4544ca8b0
(content of input bam files and index files is irrelevant)
Resulting behaviour
cwltool workflow.redundant.cwl workflow.test.json
cwltool workflow.cwl workflow.test.json
both lead to "success"
Your Environment
- cwltool version: 1.0.20180116213856