Container Linting for Modules

[JulianFlesch]

Implement linting for the wave functionality described in #3952

Linting Tasks:

Lint meta.yml

• if containers section exists: Check if docker linux/amd64 image exists (Exceptions to this for modules in https://github.com/nf-core/modules/blob/master/.github/skip_nf_test.json)
  -> Assume that we are linting for the modules repo and this file exists locally

• Check if hash part ofbuild_id (bd-this_part_1234089273409_2) matches the docker / singularity container name.

• Check for conda if the hash in build_id for the docker linux/amd64 image matches the hash in the conda lock_file

• Check for singularity and docker if the correct protocol is used: oras for singularity, http for docker

• Check for conda if lock_files exist

Lint main.nf:

• Check if container specified in main.nf matches the docker linux/amd64 image (without registry) from meta.yml "containers" section.
  -> Add functionality to fix automatically

Lint the conda lock files / environment.yaml:

• Check for conda if the dependencies + versions match / appear in the conda lock files.
  -> Look out for differneces between Python version, conda dependencies, and pip dependencies.

Where this goes

Extend the modules/lint/meta_yaml.py, modules/lint/main_nf.py files, add modules/lint/modules_containers.py

How this is used

• Add all new linting functions to modules/lint/__init__.py
• Add container linting functions to the new subcommand nf-core modules containers list (at least for testing)

[ningyuxin1999]

Thanks Julian! We haven't update the meta.yml with a "containers" section yet, right?