Fix issues in chromograph module

[fellen31]

This PR fixes some issues with the chromograph module:

• Tag being [] when not using the autozyg input
• Emit the actual files instead of the directory
• Remove prefix, it has no effect on the naming of output files from this program
• Somewhat realistic stub outputs. When not running with --euploid the actual program will output all chrs present in the input file(s) and name them according to the input files (e.g. chr1 or 1), but that's hard to replicate fully.
• More rigorous tests

PR checklist

• 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

[SPPearce]

Approve, even though the loss of the alignment in the main.nf makes me sad inside.

[fellen31]

Approve, even though the loss of the alignment in the main.nf makes me sad inside.

me too, fixed.