Command to generate pipeline container config files

[mirpedrol]

close #3953

Done:

• New function to run nextflow inspect and obtain docker config file
• New function to (re)generate all container config files
• Container config files are regenerated with nf-core modules install|update|remove

TODO:

• Add tests
• Test a lot
• What happens if the module is not found?
  • Modules form multiple repos
  • Modules included as an alias
• Is there a case where two modules have the same name but different container? how to solve this? We couldn't find an existing case of this
• Could the code be used to reduced duplication with download command?

[codecov]

Codecov Report

❌ Patch coverage is 97.01493% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.76%. Comparing base (a70e6f2) to head (bd98209).
⚠️ Report is 13 commits behind head on dev.

Files with missing lines	Patch %	Lines
nf_core/pipelines/containers_utils.py	96.29%	2 Missing ⚠️

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[mashehu]

Suggested change

	def try_generate_container_configs(directory: Path, path: Path):
	def generate_container_configs(directory: Path, path: Path):

[mashehu]

Suggested change

	workflow_directory (str | Path): The directory containing the workflow files.
	workflow_directory (Path): The directory containing the workflow files.

[mashehu]

Suggested change

	{% if multiqc %}ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it -> it[1]}){% endif %}
	{% if multiqc %}ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{file -> file[1]}){% endif %}