Fix krakenuniq build input deletion and tests

[mahesh-panchal]

Description

• Fixes a bug that deleted inputs when keep_intermediate was false.
• Updates tests to stage taxonomy files rather than the directory.

PR checklist

Closes #11557

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[mahesh-panchal]

Removed the custom_db as it seems to be required. The nf-test doesn't describe an alternate way of using this module.
The updated meta.yml from #11587 also removes "Optional".

[jfy133]

This is the one bit I'm unsure about this PR - if you are copying the entireity of the library directory, which includes 100,000s of genomes, you will massively explode the harddrive usage of the process (e.g. 200 GB of input FASTAs to 400 GB by having two times the same set of FASTA files)

This is something I was trying to avoid with the original mv operation...

[mahesh-panchal]

I've removed the dereference -L. cp -r will just copy the symlinks as is, and then the rm cleans those ups. The test with keep_intermediate = true shows the files as being correctly removed. The original symlinks remain and the input files remain intact. The copied symlinks are removed.

[mahesh-panchal]

Now why would the hash change for taxDB halfway through testing?

Edit: This is worrying. taxDB doesn't appear to be a stable artifact.