adapt pipeline to nf-schema 2.1.0

[nvnieuwk]

This PR shows an implementation of nf-schema 2.1.0 on the test pipeline. (Tests will fail because 2.1.0 has not been released yet).

Running nextflow run main.nf --help shows this:

$ nextflow run main.nf --help
Nextflow 24.04.4 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.04.3

Launching `main.nf` [hopeful_meninsky] DSL2 - revision: d17b498066



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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/testpipeline 1.0dev
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Typical pipeline command:

  nextflow run nf-core/testpipeline -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>

--help                          [boolean, string] Show the help message for all top level parameters. When a parameter is given to `--help`, the full help message of that parameter will be printed. 
--helpFull                      [boolean]         Show the help message for all non-hidden parameters. 
--showHidden                    [boolean]         Show all hidden parameters in the help message. This needs to be used in combination with `--help` or `--helpFull`. 

Input/output options
  --input                       [string] Path to comma-separated file containing information about the samples in the experiment. 
  --outdir                      [string] The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. 
  --email                       [string] Email address for completion summary. 
  --multiqc_title               [string] MultiQC report title. Printed as page header, used for filename if not otherwise specified. 

Reference genome options
  --genome                      [string] Name of iGenomes reference. 
  --fasta                       [string] Path to FASTA genome file. 

Generic options
  --multiqc_methods_description [string] Custom MultiQC yaml file containing HTML including a methods description. 

 !! Hiding 24 param(s), use the `--showHidden` parameter to show them !!
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If you use nf-core/testpipeline for your analysis please cite:

* The pipeline
  

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/testpipeline/blob/master/CITATIONS.md

[nvnieuwk]

Reference PRs:

1. Improvement/help messages nextflow-io/nf-schema#41
2. Feat/nested params nextflow-io/nf-schema#39

[mirpedrol]

Will we be able to define these function in a NF script instead of the config? Since code is not advised in config files and it might be disabled in the future.

[nvnieuwk]

I'm not sure yet, we would need to get creative here I think. I've not really given it much thought yet but I'm sure we can come up with a sensible solution. The main problem is that we need to dynamically create these files which would always need a function. AFAIK we can't access script functions in the configs?