Fix fastANI module

[Ethan-Hetrick]

PR checklist

Fixes several issues with the fastANI module:

• Replaced custom meta field for module flow control with standard meta.id fields and logic

• Added --threads $task.cpus to ensure proper multi-threading

• Made output file names descriptive

• Added stub block

• Added optional outputs

• This comment contains a description of changes (with reason).

• 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.

• Emit the versions.yml file.

• 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

[vagkaratzas]

Valiant first effort, but will require some more updates.

[vagkaratzas]

Hey! Nice, it starts to be more clear! Some more comments for additions.

[vagkaratzas]

It seems that some of the tests are failing. Try to fix linting errors locally before pushing, with the command nf-core modules lint fastani, and also use the pre-commit command when you have staged your files, before git commit.

Some output files from the tests are changing, so you will need a bit more sophisticated checks than just workflow.out.ani, since for example the all.txt file is changing during tests for tag "'sarscov2 - referece vs contigs - fastANI - all vs all mode'". Something like counting number of lines. Take other existing modules nf-tests as an example.

[vagkaratzas]

Suggested change

	process "FASTANI"
	name "Test Process FASTANI"
	tag "modules_nfcore"
	tag "modules"
	tag "fastani"
	script "../main.nf"
	process "FASTANI"

[vagkaratzas]

versions are not captured properly; it should be showing the version number here

[vagkaratzas]

you'll need to add the old 2>&1 | sed 's/version//; somehow on the eval command to properly capture the verison. See other modules for reference such as jsaminesv

[vagkaratzas]

But isnt ql_file.text now only contain the copied file q_stage path? What about the original q_src file? For many-to-many, it should include both.
Same for the reference text file below