Add process programmatic configuration

[bentsherman]

Close #4322

Example test case:

// main.nf

include { FOO ; FOO as BAR } from './module.nf'

params.outdir = 'results'
params.publish_dir_mode = 'copy'

workflow {

    FOO.config.ext.extension = 'foo'
    FOO( Channel.of('1', '2', '3') )
    FOO.out.view { "FOO: $it" }

    BAR.config.ext.extension = 'bar'
    BAR.config.publishDir params.outdir, mode: params.publish_dir_mode
    BAR( Channel.of('1', '2', '3') )
    BAR.out.view { "BAR: $it" }

}

// module.nf

process FOO {
    input:
    val(id)

    output:
    tuple val(id), path("sample${id}.${task.ext.extension}")

    script:
    """
    echo '${id} was here' > sample${id}.${task.ext.extension}
    """
}

$ ./launch.sh run main.nf
N E X T F L O W  ~  version 23.09.2-edge
Launching `main.nf` [astonishing_goldwasser] DSL2 - revision: 9b1341eb15
executor >  local (6)
[cd/f6fe43] process > FOO (3) [100%] 3 of 3 ✔
[16/d722fe] process > BAR (1) [100%] 3 of 3 ✔
BAR: [2, work/ad/d60943813d18751a8ded972ee9d798/sample2.bar]
BAR: [3, work/89/9295138db148949f054a22708895a4/sample3.bar]
FOO: [2, work/48/659fef3cb5e492e2f181c975ea232c/sample2.foo]
FOO: [1, work/db/43db80ff13d8d3c7301467e14184db/sample1.foo]
BAR: [1, work/16/d722fe4b621da24e9bd1e7f30cfd1e/sample1.bar]
FOO: [3, work/cd/f6fe432184777c0f08c9e5c1edee30/sample3.foo]

$ ls -al results/
total 1224
drwxr-xr-x  3 bent bent    4096 Oct  3 12:44 ./
drwxr-xr-x 88 bent bent   12288 Oct  3 12:38 ../
-rw-r--r--  1 bent bent      11 Oct  3 12:38 sample1.bar
-rw-r--r--  1 bent bent      11 Oct  3 12:38 sample2.bar
-rw-r--r--  1 bent bent      11 Oct  3 12:38 sample3.bar

$ cat results/*.bar
1 was here
2 was here
3 was here

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[bentsherman]

Ideally would like to merge #3793 first, then this would become part of the "Workflows" page which is more prominent.

[pditommaso]

Well done! Look @drpatelh! ☝️

[bentsherman]

I added the config setting for publishDir defaults as defined in #4186 so that I can further improve the nf-core/rnaseq POC. Doesn't have to be merged with the final PR but it's a simple change.

[drpatelh]

This is awesome! Thank you! Will take a closer look when I get a moment. Also, thanks for testing with nf-core/rnaseq!

[bentsherman]

Closing in favor of #4510