Fix gentrap report pdf



See merge request !266

Fix VEP `--failed` flag  

the `failed` flag should be a flag per the documentation
(see:
 http://grch37.ensembl.org/info/docs/tools/vep/script/vep_options.html,
and
http://oct2014.archive.ensembl.org/info/docs/tools/vep/script/vep_options.html )
But, when running, it requires a numeric value.
When running the VEP with verbose mode, it
appears that all boolean flags get converted to 1.
Therefore, I'm setting `failed` to have value 1.

This bug has been reported to Ensembl. It occurs in all versions, including most recent version 82.

@p.j.van_t_hof Should we include a failback mode, in case Ensembl fixes this in version 83?  

See merge request !267

Fix gears parse

Fixed small parse bug for the report

See merge request !265

Added a default for the retry arg

Small option to add retry by default, also can use the config to set retries now

See merge request !264

Fix shiva fails

This branch will be used to fix found issues while running functional testing of shiva.

- [x] Fix report when not executing multisamplecalling
- [x] Fix missing key when no indelrealignment and base recalibration in summary
- [x] Fix wrong sample flag for single sample variant calling
- [x] Fix name of link when sample has only 1 lib
- [x] Added settings to Shiva summary
- [x] Raise default memory
- [x] Fix concordance checks

See merge request !261

Conflicts:
	public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

the `failed` flag should be a flag per the documentation
(see:
 http://grch37.ensembl.org/info/docs/tools/vep/script/vep_options.html,
and
http://oct2014.archive.ensembl.org/info/docs/tools/vep/script/vep_options.html )
But, when running, it requires a numeric value.
When running the VEP with verbose mode, it
appears that all boolean flags get converted to 1.
Therefore, I'm setting `failed` to have value 1.

Refactoring of gears

@wyleung @h.mei 

Resolves #219, #165 and #232

Features to be added:

* [x] Kraken-report to JSON -> for html Sunflare plot display
* [x] R2, distinguish Single End or Paired End, this is used in Kraken for pairing and possible downstream alignments
* [x] Kraken-json to summary-json
* ~~[ ] Add bedtools genomecoverage (or similar tool to determine horizontal coverage and output bedgraph/wiggle)~~
* [x] Support for RNA aligners aligned bams, these may contain multiple alignments for 1 sequence. SamToFastq is not handling this.
* [x] Add report (sunflare plot)
* [x] Add tests

See merge request !241