Attention: Want an end-to-end pipelining solution for GATK Best Practices?
Does cromwell prioritise finishing workflows
Say I have a 2 task workflow
workflow A call B call C
If I start 10,000 A workflows quickly, will cromwell schedule 10,000 B calls before any C calls? (C calls start after B calls end, so I think this is the behaviour).
I think this is the behaviour and it is sensible and understandable. What techniques can I use to try to get C calls prioritised over B calls, so that the workflows start finishing sooner? Are there any built in cromwell ways to do this?
Ideas I had; have a different backend for B and C, with the C backend always prioritised over B. Or similarly have a backend parameter that does the same thing. This is a bit annoying as it starts to tie your 'portable' wdl file tightly to the backend implementation.