Create a "mkdir" utility module for Boutiques integrator
Some tools integrated with boutiques receive as an input a string which will be provided on the command line, and that string is supposed to point to an existing subdirectory. E.g.
"command-line": "supertool -out [OUTDIR] [OPT] [OPT]..."
When integrating such tools in CBRAIN, they often expect the OUTDIR to be pre-existing, and the tool crash at run time.
Historically, we modified some of these descriptor within CBRAIN so the the command was changed to
"command-line": "mkdir -p [OUTDIR] ; supertool -out [OUTDIR] [OPT] [OPT]..."
But it's kind of ugly and it means the descriptor is no longer really as generic (usable outside CBRAIN as well as within).
I suggest we implement a new utility module where a CBRAIN dev can just leave the command-line intact, and specify which input argument to run mkdir on when setting up the task.
Something like:
"BoutiquesSubdirMaker": [ "output_dir", "someinputid2" ]
Maybe the values for the configuration could instead be templates, with values subsituted from any inputs. e.g.
"BoutiquesSubdirMaker": [ "[OUTDIR]", "[OUTDIR]/[THRESHOLD]_res" ]
That woudl make the module much more flexible.