jerdra / jerdra/BOONStim

Create config utils module for managing common functions in config

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config good first issue maintenance
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Description

Some groovy code snippets are duplicated across config files. For example the snippet:

```
Closure get_partition;
if (partition instanceof Closure){
get_partition = partition
}else{
get_partition = { t -> partition }
}

Closure cacheDir;
if (params.cache_dir){
cacheDir = { f ->
def d = new File("$params.cache_dir/$f")
d.mkdirs()
"$params.cache_dir/$f"
}
}else{
cacheDir = { f -> "" }
}
```

Is re-used in multiple config files. Originally thought to define all config specs in the main `boonstim.nf.config` file but the scope induced by ` includeConfig` doesn't seem to carry over function definitions - they are local.

The solution here would be to create a groovy script containing function definitions that can be imported in each of the config files.

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