POC: module yaml restructure

[ewels]

Proof of concept showing minor change to the parsing of module processes, to correctly capture structure of inputs. Currently just dumps a hypothetical YAML string to the console when running linting, eg:

nf-core modules lint affy/justrma

input:
- - meta:
      type: val
  - samplesheet:
      type: path
  - celfiles_dir:
      type: path
- - meta2:
      type: val
  - description:
      type: path

Just a starting point. If we want to fix all module metas, needs a lot more work:

• Change how meta.yml is built when creating a new module from the template
• Update the linting code to expect this structure when checking existing modules
• Do all of the above for output as well as input
• Find and fix all the edge cases
• Update the website documentation pages to understand this format
• Update the developer docs
• Check where else meta.yml is used and update accordingly
• Somehow try to migrate all 1k modules to the new format, without losing custom data added by hand 😰
  • Note that even though the structure is different, the named keys should be the same. So hopefully can automate.

Related / would fix:

• Add new modules subcommand "update-meta-yml" #1555
• Modules update: Warn if input channels change #1993

[ewels]

Created an issue to track this in the modules repo: nf-core/modules#4983

[pditommaso]

Good timing! we need to discuss about this, meta.yml is becoming essential to unlock multiple critical features (types checking, output schema, generative workflows), I think we need to promote it as a nextflow "standard"