Restructure output directory

[nvnieuwk]

Description of feature

The output directory should be restructured to allow incremental file writing in the same directory over multiple runs.

<params.outdir>
  - <pipeline_version>_<date> => Contains pipeline run specific files
  - <family1>
    - <sample1>_<pipeline_version>_<date> => contains all sample specific files
    - <sample2>_<pipeline_version>_<date>
    - joint_<pipeline_version>_<date> => contains all family specific files
    - qc_<pipeline_version>_<date> => contains all qc for the family specific files (multiqc)
  - <family2>
  - ...

A separate multiqc should be created for the whole run and separately for each family.