Docs required

Documentation required settings and flags for pipelines. Now includes the new reference module (e.g. `reference_fasta`) and tries to name namespaces correctly. See #161 (and to a lesser extend #163)

See merge request !174

Force logging to a file

see #158

See merge request !175

Change bwa to bwa-mem

part of #129

See merge request !173

Added executables that are missing on a native osx install

Was installing ide on new mac book and did see some issues in the unit tests

See merge request !171

Fix for issue #167

See merge request !172

NO more reflective issues, simplify some refs.

Remove reflective calls within GearsTrait.

See merge request !170

Feature gears (metagenomics)

Metagenomics pipeline, start from bam or from FastQ files.

Dependencies:
- Sambamba (v0.5.1+)
- Kraken

See merge request !168

Feature yamsvp

Merging into develop to change the extensions/tools section

keep yamsvp branch for development!

See merge request !122

Update code to v0.4 branch and fix usage of Ln and memory settings of VMEM, settings for memory will be committed to the shark-config branch with recommended defaults.

Feature reference

Part of issue #81

This is only checking and not auto generating anything. Adding auto generate is now not a lot of work anymore.

See merge request !147

add more info to VepNormalizer tool help

self-explanatory.

See merge request !157

Feature vcfanotate

Adding a feature for project

See merge request !167

shift option had wrong var name

See merge request !155