Add log file in output channels of umitools/dedup

[anoronh4]

Added log file parameter and output channel, and updated all pytests to check for the log file output.

PR checklist

Closes #3505

• 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.
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• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
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  • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

[nvnieuwk]

Can you merge all changes to umitools/dedup in one PR? That will save you the hassle of having to solve merge conflicts and it's easier to review :) Thanks!