Flexible AdapterRemoval

[apeltzer]

This is based on @maxibor and @jfy133 s work and help and should provide the means to run:

• AdapterRemoval v2 on PE/SE data
• with or without read merging /collapsing
• with or without read trimming
• Skipping the entire module if no need for the module in general.

Thereby addressing #137, #64.

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

This might require some docs updating (open a PR against the ar_optional branch here) and some more testing, as I adjusted some stuff in my PR on top of @maxibor 's.

Thanks A BUNCH for helping out on this both!

[phue]

Nice work!
This is just a bit of nitpicking, also I noticed the somewhat inconsistent use of adapter vs. adaptor.
I know different tools use different spellings but I think it would be nice to have it consistent for the pipeline params

[apeltzer]

I'll be cleaning up the trimming part - its possible to have a predefined command in there for SE/PE mode and get rid of some boilerplate code this way 👍

[apeltzer]

Unfortunately, the output handling with AdapterRemoval makes it a bit complicated to be able to accomodate all cases (PE/SE) into a single condensed version:

• depending whether you run with --collapse, its creating different fastq files as output
• depending on whether you use the trimming, the same happens as well

So I can't really combine individual steps in all cases, but rather have the same merging and quality trimming options in externalized commans that I use in all cases (which works fine 👍 ) to make the code a bit cleaner and easier to read.

I guess once the tests pass, we can basically assume this is fine 👍