Output collection and intermediary files

[milos-ljubinkovic]

We could potentially create a new configuration field that would look something like this:

option 1: Leave all created files where they are created (engine.delete_intermediary_files=false currently)

option 2: Delete intermediary files as the workflow is executed (engine.delete_intermediary_files=true currently)

option 3: After the workflow is completed delete all the files except the outputs and put the outputs in the same directory

[vladimirkovacevic]

Hi @milos-ljubinkovic , Firstly, I would separate this into two issues. I understand that its implementation is connected, but from users perspective they seem different. First issue - intermediary files option 1: Leave all created files where they are created (engine.delete_intermediary_files=false currently) option 2: Delete intermediary files as the workflow is executed (engine.delete_intermediary_files=true currently) option 3: After the workflow is completed delete all intermediary files

Second issue - Output collection option 1: Collect all outputs in the same directory option 2: do nothing (their paths are listed in output json)

P.S. Is it possible to write cwl.output.json to file?

[bogdang989]

I was in process of writing nearly the same thing as Vladimir :) Agree

[teodora-aleksic]

I agree as well.