Pmdtools addparams

[jfy133]

Adds additional PMDtools functionality - adding --pmdtools_first and --pmdtools_platypus, at the request of @pontussk, and some additional cleanup.

Also includes an additional pmdtools/trimbam only check to resolve #349

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 necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md

[apeltzer]

Lets keep this for a while - wait for TSV and merge this to TSV. Then we can do the 2.2 Ulm release soon :-)

[jfy133]

Actually I say we push it back to 2.3, to keep tSV lean, and as we've not recieved any more feedback yet exactly how to structure the requested parameters.

[apeltzer]

Fine by me! :-)