Task aliasing

Occasionally, you will need to call the same task multiple times within the same workflow. For example, you might need to run the same variant caller between two samples to determine the variants that are unique to one. Another interesting use case might be to run the same variant caller on the same sample with different parameters to examine the differences. In these cases, you'll want to reach for task aliasing to ensure that the names for each call remain unique.

This often takes a form similar to the following example.

# ... task definitions ...

workflow run {
    # `taskA` is run twice—this is enabled using task aliasing.
    call stepA as first {}
    call stepA as second {}

    # `taskB` takes in the output from the `first` task.
    call stepB { input: in = first.out }

    # `taskC` takes in the output from the `second` task.
    call stepC { input: in = second.out }
}