Added wigle and tdf files to summary



See merge request !361

Fix names

When jenkins find no issues here we can merge this

See merge request !359

Fix small fixes



See merge request !357

General refactor Biopet



See merge request !358

Fix: Show a message for those plot, which were not created by FastQC. Some stati…

…stics cannot be collected by FastQC such as Kmer when the sequences are clean.

See merge request !355

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: Show a message for those plot, which were not created by FastQC. Some statistics cannot be collected by FastQC such as Kmer when the sequences are clean.

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