Step 16 - Where to put params?

We want the output filename to be configurable. That means that we either use the params map for this (and take care it is available in modules that are included) or we pass it to the process as part of the input. Let us explore both scenarios.

But first, we need to understand a bit better where the contents of params comes from. We already covered a few examples where we specify a params key on the CLI. There is another way as well, via nextflow.config. In it, we can add a scope params and add the configuration there.

Let us reconsider the previous example (step15) but this time add a nextflow.config file like this (please update the <...> part according to your situation):

params.input = “$PWD/data/input?.txt”

Let us illustrate the effect by means of two examples:

> nextflow -q run . -entry step15
WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
[input3, <...>/work/d3/3b7016780d0a10bc43a4a1e303edbc/output.txt]
[input1, <...>/work/e8/52a69a6234d9008041151f0ddaea06/output.txt]
[input2, <...>/work/c9/ff527e7934c309ec34ee4fabdf0654/output.txt]

> nextflow -q run . -entry step15 --input data/input1.txt
WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
[input1, <...>/work/4a/9479b71506cc1ca0c536ad587498af/output.txt]

In other words, params can be defined in nextflow.config but if it appears on the CLI then the latter gets priority. Please be reminded that params is a map, the following is equivalent:

params {
    input = "/.../diflow/data/*.txt"
}