Fastavalidator topics migration

[EfraMP]

PR checklist

Partially closes #10832

• Update topics migration.
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Broadcast software version numbers to topic: versions - See version_topics
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[EfraMP]

The conda failure seems to be pre-existing. The CI runners fail the pkg_resources, but the Docker and Singularity checks pass. What to do??

[camlloyd]

The conda failure seems to be pre-existing. The CI runners fail the pkg_resources, but the Docker and Singularity checks pass. What to do??

Attempt to fix upstream in bioconda/bioconda-recipes#63515

[EfraMP]

The conda failure seems to be pre-existing. The CI runners fail the pkg_resources, but the Docker and Singularity checks pass. What to do??

Attempt to fix upstream in bioconda/bioconda-recipes#63515

So then what? I wait for your PR to be merged to Bioconda??

[camlloyd]

Could you please re-run:

nf-core modules lint fastavalidator --fix
nf-core modules test fastavalidator --update

[EfraMP]

Done. The current conda checks continue to fail

[camlloyd]

Suggested change

	// Exit if running this module with -profile conda / -profile mamba
	if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
	error "Fastavalidator module does not support Conda. Please use Docker / Singularity instead."
	}
	def prefix = task.ext.prefix ?: "${meta.id}"

[EfraMP]

Got it, but messed up the branch tracking...

Opened a new PR in #10925