Setting non-default parameters

[davidwedge]

When running in 'germline' or 'cell_line' mode, many of the parameters are set to hard-coded values in 'Battenberg.R'. This means that it is impossible for users to set alternative values when running in these modes.

[christopherwirth]

@denizecek David mentioned that you are working on this for your samples without matched normals.

I think it should be solvable by adding an if (missing(variable_name)) { variable_name=... } condition before the new defaults are defined in germline/cell_line mode. In battenberg.R on the master branch, this would be on each of the following lines:
134-138
140
142-145
148-152
154-158

See the following example for proof of concept:

test_func = function(a = 1, b = 2) {
  if (missing(b)) { p = 3 }
  a + p
}

test_func(a = 2)
[1] 5

test_func(a = 2, p = 2)
[1] 4

Obviously the above example would be silly on its own because there in no point in b having a default value. But in Battenberg I think it makes sense to have a general default value, but for certain modes say: "if we are in mode x and the user has not specified a value for this, use a different default value instead"