Fix vcffilter extension



See merge request !335

Added function dataprovider

This is my dataprovider for this test. If you have quotations, please let me know.

See merge request !339

Fix basecounter executable



See merge request !341

Added check on no readgroups

Fixes #289 

See merge request !342

Feature dustbin report

Fixes #288 

See merge request !340

Fix for gears single end bam files

Fixes #287 

See merge request !337

Feature skip abort

This adds the possibility to force the pipeline to continue with a config value even when the Fastqvalidator finds a problem.

This merge request depends on !326 

See merge request !333

Added fix mpileup for bcftools

fixes #278 

See merge request !326

bow authored 9 years ago and Peter van 't Hof committed 9 years ago

As mentioned in the documentation[1], the `--custom` flag can
be specified multiple times.

[1] http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_custom
(cherry picked from commit 5204f4f)

Added check on sequence dictionary

Fixes #283 

See merge request !325

Feature tagging

Fixes #254 

See merge request !334

Seqstat reporting read length histogram

Added reporting of readlength histogram as `stats > reads > len_histogram`
Simplified / Scalafied some of the SeqStat code

Adding more unit tests

Fixes #284 

See merge request !331