miniwdl icon indicating copy to clipboard operation
miniwdl copied to clipboard

scatter variable name collision policy

Open mlin opened this issue 4 years ago • 0 comments

Cromwell allows a scatter variable name to collide with another value elsewhere in the workflow. Inside the scatter body, the scatter variable shadows the other value.

e.g. this is fine:

version 1.0
workflow hello {
    input {
        Array[Int] y = range(3)
    }
    scatter (y in y) {
        Int x = y+1
    }
    output {
        Array[Int] x_out = x
    }
}

seen in the wild in:

https://github.com/biowdl/jointgenotyping/blob/81881f21506983a917d4dc433c6b326443abe275/jointgenotyping.wdl#L45-L48

miniwdl rejects these. Is this a spec issue? or a validation oversight in Cromwell?

mlin avatar Aug 10 '19 03:08 mlin