resources.yaml

### SPECIFY THE RESOURCES FOR EACH RULE.

### THIS IS ONLY REALLY NECESSARY IF YOU PLAN ON RUNNING THE VARIANT CALLING ON A CLUSTER (WHICH IS LIKELY WHAT YOU WANT TO DO)
### EACH INDIVIDUAL RULE WILL BE SUBMITTED AS ONE JOB WITH THE RESOURCES THAT YOU SPECIFY HERE.
### AS SOON AS ONE RULE FINISHES, THE NEXT JOB (i.e. RULE) WILL BE SUBMITTED.
### THIS SIGNIFICANTLY IMPROVES PERFORMANCE AND CLUSTER USAGE, BECAUSE RESOURCE REQUIRMENTS CAN BE TAILORED TO SPECIFIC RULES

### THE RESOURCES BELOW WERE TESTED FOR A 147GB BAM FILE WITH 1.966.058.362 READS
### THE RESOURCES YOU REQUIRE MIGHT DIFFER SIGNIFICANTLY DEPENDING ON THE ARCHITECTURE OF YOUR CLUSTER,
### BUT THE SPECIFIED VALUES HERE MIGHT SERVE AS A SORT OF GUIDELINE FOR INITAL TESTING

runtime: # has to be specified in min
  BaseRecalibrator: 180
  GatherBQSRReports: 5
  ApplyBQSR: 180
  GatherRecalBamFiles: 120
  SortBam: 300
  IndexBam: 180
  HaplotypeCaller: 600
  MergeHaplotypeCaller: 70
  CombineGVCFs: 300
  GenotypeGVCFs: 300
  MergeCohortVCFs: 60
  VQSR_indel: 30
  VQSR_snp: 45
  ApplyVQSR_indel: 10
  ApplyVQSR_snp: 10
  SelectVariants: 5
  VEP: 1000


memory: # has to be specified in MB
  BaseRecalibrator: 50000
  GatherBQSRReports: 5000
  ApplyBQSR: 45000
  GatherRecalBamFiles: 5000
  SortBam: 40000
  IndexBam: 5000
  HaplotypeCaller: 80000
  MergeHaplotypeCaller: 10000
  CombineGVCFs: 85000
  GenotypeGVCFs: 40000
  MergeCohortVCFs: 10000
  VQSR_indel: 15000
  VQSR_snp: 15000
  ApplyVQSR_indel: 6000
  ApplyVQSR_snp: 6000
  SelectVariants: 5000
  VEP: 15000


threads:
  BaseRecalibrator: 15
  GatherBQSRReports: 2
  ApplyBQSR: 25
  GatherRecalBamFiles: 2
  SortBam: 10
  IndexBam: 16
  HaplotypeCaller: 25
  MergeHaplotypeCaller: 2
  CombineGVCFs: 10
  GenotypeGVCFs: 15
  MergeCohortVCFs: 5
  VQSR_indel: 3
  VQSR_snp: 3
  ApplyVQSR_indel: 3
  ApplyVQSR_snp: 3
  SelectVariants: 3
  VEP: 40