Feature/reduce delivery footprint

NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework

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Feature/reduce delivery footprint #73

Closed b97pla closed 8 years ago

b97pla commented 8 years ago

Fixed calls to snpEff (RAM, skip intermediate files, compress output)
Option to include/exclude OQ, BD and BI tags during bam recalibration
Option to remove recalibrated bam from final output
Fixes to processing BAMs when splitting using ParallelShell
Fixes to handling intermediate files and some un-annotated output files (mostly index files)

johandahlberg commented 8 years ago

Looks cool to me. It's a bit difficult to review - but I assume that this has been tested and all is alright. Let me know if you think it's necessary that I look into it more deeply otherwise I feel comfortable merging.

b97pla commented 8 years ago

@johandahlberg This should be good to go, travis is probably complaining which may be related to set running out of RAM?