Ruben Vorderman
Ruben Vorderman
> @rhpvorderman Are you suggesting to add some method to resort to a tasks/workflows default? Like a function which will cause the input to be omitted if the value given...
Hmm. Or should that be implicit? s_override is not defined, so omitted by default.
:+1: From me.
> Using environment variables circumvents this issue ..." > "Environment variables are not usable within other WDL expressions" Due to environment variables not being usable in WDL expressions, that limits...
@mlin. Agreed. Redesigning WDL to *only* use environment variables and deprecate the templating is the better option. > Re "Environment variables are not usable within other WDL expressions" -- I...
> Are there any use cases which would get worse if this were the case? Supplying optional variables comes to mind. Where you can do `~{"--optional-flag " + optional_value}` now....
And another thing that is hairy: How to work with tools that use the same flag multipe times to specify output files. For instance `-o output1.fastq.gz -o output2.fastq.gz -o output3.fastq.gz`....
@patmagee, my primary comment is that I think this is a inverse approach by requiring the maintainer to put env in front off **everything** to make sure no shell code...
I have been thinking somewhat more about this and I start to wonder: what does this feature protect you from that containerization does not already? If users can submit their...
Thanks for the further clarification on the security impact. I am in favour of adding this feature and I hope we can find an ergonomic way to implement this. >...