update JSON schema for subworkflows meta.yml

[mirpedrol]

Update the JSON schema to validate subworkflows meta.yml. This adds the structure field to describe the structure of input and output channels.

input:
  - ch_fasta:
      description: A channel containing the reference fasta file.
      structure:
          - meta:
              type: map
              description: meta map
          - fasta:
              type: file
              description: fasta file
              path: "*.fasta"
  - ch_fai:
      description: channel containing fasta.fai file
      structure: 
          - meta:
              type: map
              description: meta map
          - fai:
              type: file
              description: fasta.fai file
output:
  - versions:
      description: channel containing software versions file
      structure:
          - versions.yml
                type: file
                description: file containing versions of the software used
  - mutect2_vcf:
      description: Channel containing a list of compressed vcf files
      structure:
          - meta:
              type: map
              description: meta map
          - vcf:
              type: file
              description: vcf file 

[mirpedrol]

@nf-core-bot fix linting

[github-actions]

Nothing for me to do here! 🤷
This is probably because the linting errors come from nf-core lint and have to be fixed manually (or with nf-core lint --fix).

[nvnieuwk]

LGTM!

[mirpedrol]

I have decided to update some subworkflows to test the JSON file and have them as examples.
I was hoping that it wouldn't take too much and I could update all of them but let's see where do we get 😉

[mashehu]

If you could add the language-server link to the json schema at the start of all files to so we start adding them, that would be great

[mirpedrol]

Merging this to a dedicated branch subworkflows_meta_yml, the idea is to work on this branch during the hackathon and then merge this to master.