Flexible trimming of bams based on library type

[TCLamnidis]

Description:

1. Fixed a bug where evaluation of boolean options was interpreted as string, which caused these options to always be on (e.g. trimbam softclipping). @jfy133
2. Replaced left and right trimming parameters with library specific left and right parameters. It is now possible to trim hUDG libraries e.g. 2bp on each side and nonUDG libraries e.g. 7bp on each side within the same eager run. Should provide more robust genotyping and easier way to exclude damage without throwing away data.
3. Added def before definitions of variables including ifelse clauses, for clearer definitions.
4. Renamed pmdtools test in CI. WAs erroneously tagged TRIMBAM. Now it is PMDTOOLS.

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!
• Ensure the test suite passes (nextflow run . -profile test,docker --paired_end).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

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