pipe_multiple_processes.md

Piping with multiple processes at the same time

You should know that pipes are very useful in Nextflow! You can chain lots of things through pipes, which makes the code much more readable. See an example below:

Channel
  .of(1..10)
  | SUM_10_TO_EACH
  | FILTER_OUT_EVEN_NUMBERS
  | view()

However, it could be that you're in a situation where you want a channel to be fed to two processes and then you want to do something to the output of both processes. Let's think simple here: You just want to turn these two output channels into one, knowing that each process did a different thing to the original channel. There's a long version to do that. You will see it below:

Channel
  .of('a'..'z')
  | FIRST_PROCESS

Channel
  .of('a'..'z')
  | SECOND_PROCESS

FIRST_PROCESS.out
  .mix(SECOND_PROCESS.out)
  | THIRD_PROCESS

You don't have to do it like that. There's a much nicer way:

Channel
  of('a'..'z')
  | FIRST_PROCESS & SECOND_PROCESS
  | mix
  | view()

If you're a one-liner, you can make it even shorter, but I like it this way 😃

In this example, our THIRD_PROCESS has a single input and that's why we used the mix channel operator to put together the two output channels, one from FIRST_PROCESS and one from the SECOND_PROCESS. You can remove the mix if you want, but then you'd have to change the code of the THIRD_PROCESS to expect two input channels, like in the snippet below:

process THIRD_PROCESS {
  debug true

  input:
    val x
    val y

  output:
    stdout

  script:
    """
    do_something_here
    """
}