engine function to map over an Array

[ruchim]

There's currently one main function (prefix) that maps over all the elements in an array. When one wants to do some other kind of mapping/manipulation over all the elements in an array, they can do so by using a scatter block:

Array[String] arr = ['a', 'b', 'c']

scatter (i in arr) {
 String append_suffix = i + '_1'
}

Array[String] arr_with_suffix = append_suffix # ['a_1', 'b_1', 'c_1']

It would be great if there was an engine function that allowed for running functions over an Array type without requiring the boilerplate of a scatter block.

[cjllanwarne]

Just a thought, what would you think of a list comprehension expression, eg something like the python syntax? (just throwing out some ideas here):

# 1:
Array[String] arr_with_suffix = [ a in arr: a + "_1" ]
# 2:
Array[String] arr_with_suffix = [ arr: a => a + "_1" ]
# 3:
Array[String] arr_with_suffix = [ map arr: a => a + "_1" ]
# 4:
Array[String] arr_with_suffix = [ a + "_1" for a in arr ]

[ruchim]

A list comprehension sounds exactly like whats required, and I could work with any of that syntax.

Do you imagine something like this would be allowed? Array[String] arr_with_suffix = [ a + "_1" for a in arr if (true) ]

[cjllanwarne]

@ruchim if we go down this route, I don't see why not!

[dheiman]

Another possible suggestion is to follow the path of vectorized languages like R or MATLAB (which in my experience are the two most common languages used by bioinformatics researches), and simply have functions be Array-aware. That is, if a scalar function that takes scalar input is run on an array, a new array is returned with each value being the result of that scalar function being run on the corresponding value of the input array (implicit map).

[illusional]

I raised an issue which ended up being a duplicate but wanted to quote @jtratner answer from here:

scatter(x in arr) {
   String names = basename(x)
}
call mytask (input: names=names}

and then names outside of scatter are an array of strings.

[ghost]

Super convenient for array of maps of file with their indexes, i.e. array of bams and their bai.

[illusional]

Hey @patmagee, is there any way to gain some momentum on this feature request? Is list comprehension an acceptable approach? I'm happy to target something against a spec and implement it in MiniWDL maybe?

[vortexing]

I like the addition but I'd opt for the less burdensome (on the user) approach suggested by @dheiman where if you pass an array of strings to something like basename or a +, you'd get the same array back, in the same order, but with the operation performed. That way folks who aren't python users don't need to learn what list comprehension is.