Feature fix missing values

Fix for wrong messages when config value does not exist

Now also fix for #112

See merge request !89

Make a val for globalConfig, test should now be able to override it so unit test are not depending on a global var

Patch flexiprep fastqc

Found another bug because of incorrect type usage, which makes the pipeline output paths like `/my/path/Some(file.txt)` when it should be `/my/path/file.txt`. This pull request should fix it.

See merge request !91

Patch flexiprep parse adapters

This addresses the bug (not reported) where the adapters are incorrectly supplied to cutadapt. To protect against it, unit tests were added, and some refactoring was done.

See merge request !82

Feature add ids to filter

Added options to vcf filter tool for @s.a.j.van_der_zeeuw and @j.f.j.laros

See merge request !88

Feature fix raxml

Small fix for basty pipeline

See merge request !87

Patch flexiprep mapping flags

@wyleung and @p.j.van_t_hof

This is what we discussed earlier. The temporary solution is to expose it in the command line. I've also added some notes there and did some small refactoring. It's all in the commit messages :).

See merge request !80

Patch doc fixes

Part of the docs in develop are still in there old setup. Should be added to dev.

See merge request !86