Reduce complexity in CytoSnake scripts

[axiomcura]

Mentioned in #37 in this comment

The script design is unnecessarily complex, since we are only using a single function call; therefore it should be encapsulated into a single main() function to reduce complexity instead of two.

Example:

import cytotable

def function1(param1, param2, param3):
   # enter code here 
   cytotable.convert(param1, param2, param3)
   return 0


def main ():
   p1 = snakemake.param[0]
   p2 = snakemake.param[1]
   p3 = snakemake.param[2]

   function1(p1, p2, p3)

if __main__ == "__name__"
   main()

can be reduced to:

def main ():
   p1 = snakemake.param[0]
   p2 = snakemake.param[1]
   p3 = snakemake.param[2]

   function1(p1, p2, p3)

if __main__ == "__name__"
   main()

Todo list

• Make CytoSnake conda installable Making CytoSnake Conda Installable.  #78
• Unable to import cytosnake helper functions causes repetitive code within workflow scripts #18
• Allow whole config loading to scripts instead of partial loading.  #81
• Develop a function that searches for plate map based on given plate name.  #83

[axiomcura]

small update regarded about this issue:

turns out that sectioning parameters is not ideal for instances where there are two functions used from the same parameter. Therefore the best approach is the load in the whole configuration instead of sectioning it.

First we the scripts have to be designed in order for it to be simple enough to allow whole config integration.