Merge remote-tracking branch 'remotes/origin/release-0.4.0' into develop

docs/config.md

docs/general/config.md

docs/pipelines/basty.md

docs/pipelines/flexiprep.md

docs/pipelines/mapping.md

docs/pipelines/shiva.md

docs/release_notes_0.3.1.md

docs/release_notes_0.3.2.md

docs/release_notes_0.4.0.md

docs/tools/SamplesTsvToJson.md

mkdocs.yml

pom.xml

protected/biopet-gatk-extensions/pom.xml

protected/biopet-gatk-pipelines/pom.xml

protected/biopet-protected-package/pom.xml

protected/pom.xml

public/bam2wig/pom.xml

public/bammetrics/pom.xml

...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala