Step 19 - Use a closure

We mentioned that there are 2 ways to pass an output filename to a process. There is a third one, using a closure or function to handle the naming for us.

Let us illustrate this with an example again:

// Step - 19
def out_from_in = { it -> it.baseName + "-out.txt" }
process process_step19 {
    publishDir "output"
    input:
        tuple val(id), file(input), val(config)
    output:
        tuple val("${id}"), file("${out}"), val("${config}")
    script:
        out = out_from_in(input)
        """
        a=`cat $input`
        let result="\$a + ${config.term}"
        echo "\$result" > ${out}
        """
}
workflow step19 {
    Channel.fromPath( params.input ) \
        | map{ el -> [
            el.baseName.toString(),
            el,
            [
                "id": el.baseName,
                "operator" : "-",
                "term" : 10
            ]
          ]} \
        | process_step19 \
        | view{ [ it[0], it[1] ] }
}

The result is as follows:

> nextflow -q run . -entry step19
WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
[input2, <...>/work/a3/2c69f0be071c1e2170a19f6f397dda/input2-out.txt]
[input3, <...>/work/0a/e2dc41121ad3b619348d3abc985839/input3-out.txt]
[input1, <...>/work/04/18d42a25a1923a3ff15cf5f6a7aae8/input1-out.txt]

We can even add the closure to the configuration map sent to the process, but NextFlow complains that this is not serializable so you may miss some features and most importantly it may not work at all times:

WARN: Cannot serialize context map. Cause: java.lang.IllegalArgumentException: Unknown workflow parameter definition: map -- Resume will not work on this process

This approach may seem like completely over-engineered but for a lot of use-cases it turns out to be a good fit. Although, not in the way we introduced it here. We come back to that later…

A DiFlow module contains a function definition that takes the input file name as input and generates an output filename.