Fix small fixes

Fixes #299 and #300 

See merge request !353

add amplicon bed file documentation

Added documentation about amplicon_bed and regions_of_interest bed files.

closes #297 

See merge request !356

Fix bug when bowtie2 is not able to find reference files ending with .bt2l



See merge request !354

Fix bug when bowtie2 is not able to find reference files ending with .bt2l (new large file definition)

Fix compile issues



See merge request !352

Feature small rna

smallRNA pipeline TinyCap

closes #237 
closes #258 
closes #265 
includes fixes for !306

See merge request !312

Seqstat: length array was too short for keeping the readlengths.

the array was too short

See merge request !349

Feature carp docs 0.6.0



See merge request !350

Fixed biopet logging

Fixes #293 

See merge request !351

Feature mergesvcalls

This branch will introduce the SV-merging tool for the VCF files generated by SV-callers in the ShivaSVcalling pipeline.

We now use the PySVtools made by @wyleung 

closes #236

See merge request !301

Feature toucan summary



See merge request !338

Fixed default value

Fixes #294 

See merge request !347

Feature docs 0.6.0

TODO:

- [x] ***Gears*** pipeline needs an example config
- [x] ***Gentrap*** refactored
- [ ] ***Toucan*** needs an disclaimer: When used with the Varda Db it assumes 2 vcf files as input
- [ ] ***Shiva*** add reference_fa to Required settings (maybe in all pipelines)
- [ ] ***Shiva*** add all variantcallers to the list of available variantcallers
- [ ] ***Shiva*** explain about public / private version of Shiva
- [ ] ***ShivaSVCalling*** 
- [ ] ***TinyCap*** add new documentation about the smallRNA pipeline.
- [x] ***Developer docs*** solves #261 - missing paragraph about the config and example code to implement using of the `config` in extensions/pipelines


Fixes #261 and #264

See merge request !315