Dear all,

I (finally) started transitioning our lab’s tools from using parallelism (the 
multi-splitter) towards collections. In the parallelism scenario, tools were 
run in their respective working dir, resulting from a chdir performed in 
extract_parts.sh. That was nice. But I see when using collections that there is 
a workdir around, but the tool is not actually run in it. I often need to 
symlink to change input file extensions and can’t imagine noone else does that, 
so I wondered if I was missing something. If I’m not, then here’s my two 
questions:

- Is there an accepted place to symlink files in (and how do I pass the working 
dir in a tool XML)? I don’t want them in the files/ dir, looks bad, they’re not 
cleaned, etc etc.
- Would it be a bad idea to make tools run inside a workdir, apart from 
possibly breaking backwards compatibility?

cheers,
— 
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden



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