Module meta.yml restructure

[mirpedrol]

Continuation of #2789

This PR adds an automated way of generating the right format meta.yml for modules.

 input: 
   - - meta: 
           type: map 
           description: | 
             Groovy Map containing sample information 
             e.g. [ id:'test', single_end:false ] 
       - scaffold: 
            type: file 
            description: Fasta file containing scaffold 
            pattern: "*.{fasta,fa}" 
   - - fasta: 
           type: file 
           description: FASTA reference file 
           pattern: "*.{fasta,fa}" 

Note that the structure proposed in nf-core/modules#4983 (comment) is not possible if we want to automate the creation of this file, as comments are ignored when reading a yaml file with Python.

Example of outputs formatting:

output:
  - versions:
    - "versions.yml":
        type: file
        description: File containing software versions
        pattern: "versions.yml"
  - bam:
    - meta:
        type: map
        description: Groovy Map containing sample information
  
    - "*.bam":
        type: file
        description: Sorted BAM/CRAM/SAM file
        pattern: "*.{bam,cram,sam}"

In this PR we also add an option --update-meta-yml --fix to fix existing files automatically.
To be changed to --fix as suggested in #2789 (comment)

Pytests are also missing for this functionality.
A test was added for the command nf-core modules lint --fix. ⚠️ This test will fail until the JSON schema is updated (nf-core/modules#5837)

Together with this PR, there are other actions which must happen at the same time:

• Updating the JSON schema used for lining module and subworkflows meta.yml files update JSON schema for modules meta.yml modules#5837
• Update the documentation
• Add the same changes for subworkflows
• Add a mention of bio.tools and EDAM ontologies for inputs and outputs Modules meta.yml ontology #3032

POC in modules: nf-core/modules#5867

[mashehu]

Note that the structure proposed in nf-core/modules#4983 (comment) is not possible if we want to automate the creation of this file, as comments are ignored when reading a yaml file with Python.

Looked into the pyaml issue, and looks like some people are using ruamel instead of pyaml. Should we do the same?

[mirpedrol]

Looked into the pyaml issue, and looks like some people are using ruamel instead of pyaml. Should we do the same?

Sounds good!
I changed to ruamel in the follow-up PR because it was the best way to keep the proper indentation. But the comment is still not ideal because it moves it to the line above.

# tuple
- 
    - meta

You can see how the changes in some modules will look like here.

[mirpedrol]

I will close this PR because I fixed the merge conflicts in the follow-up one #3032, #3032 is the definitive PR 😄