Peter Amstutz

CWL has a concept of "secondary files" for exactly this purpose (although secondary files are an attribute of File, not Directory.) I agree with the idea of a bundle being...

I would be +1 for having only bundles, as it would align better with the Arvados model of collections.

Technically, CWL doesn't require searching for secondary files except as a convenience for the submitter. The submitter (client) can provide secondary files explicitly.

However I think DRS would greatly benefit from a general pattern for describing dependencies of a file (because if it doesn't have it, that need doesn't go away, instead client...

I agree with this, I proposed exactly something like this for WES several years ago, unfortunately I don't have the presentation from then. It didn't go anywhere, people didn't seem...

It doesn't use unshare because I wasn't familiar with it when I wrote that part of cwltool. I was mainly thinking about how you can enable/disable network access for Docker...

Reported on discord: > I tried to generate a seed with both generated earth cave and generated waterfall, but it can't satisfy incentive placement doing that. Turning off waterfall and...

`npm install [email protected]` should also work ([email protected] is the version that depends on the problematic version 2.7.1 of the `rrule` library).

Here's a few design sketches: # Explicit metadata propagation Tool specification: ``` inputs: fq: File outputs: bam: type: File outputBinding: addMetadata: $(inputs.fq.metadata) ``` Input document: ``` fq: class: File metadata:...

Via $schemas (which probably should have been called $ontologies) we could enable the user to provide OWL mappings between ontologies.