run clean as TwoCoreJob to allow more RAM, only separate indels and s…

NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework

9 stars 9 forks source link

Closed b97pla closed 7 years ago

b97pla commented 7 years ago

…nps if actually doing recalibration

This PR introduces two changes:

The amount of RAM assigned to the IndelRealigner step is doubled (corresponding to two cores)
The raw vcf is only separated by snp and indels if recalibration of variant qualities is performed

Functionality has been verified on Milou.

johandahlberg commented 7 years ago

This looks good to me. Unless @vezzi has some objections I can merge it.

vezzi commented 7 years ago

looks fine. @b97pla you want @sylvinite to deploy it first on stage and run it through the test he has been writing?