broadinstitute / palantir-workflows

Utility workflows for the DSP hydro.gen team (formerly palantir)

broadinstitute/palantir-workflows Issues

Add pipeline for benchmarking SVs
Closed 5 months ago3
SimpleBenchmark doesn't run without providing evaluation bed file
Closed 7 months ago1
Ordering issues in PCATasks.ProjectArray
Closed 8 months ago1
plink2 --set-all-var-ids in PCATasks.ArrayVcfToPlinkDataset
Updated 8 months ago
RAM allocation in plink2
Updated 8 months ago
Disk size in PerformPopulationPCA
Closed 8 months ago1
Exposing the number of cores in PerformPopulationPCA
Closed 8 months ago1
Replace ${basename} with ~{basename} in PerformPCA
Closed 8 months ago1
Single core tasks in PerformPopulationPCA
Updated 9 months ago
Add an error message/potentially rethink this error check
Closed 9 months ago4
FunctionalEquivalence: Passing information through file names
Updated 9 months ago
FunctionalEquivalence cannot handle data with no QUAL < 30 calls made
Updated 9 months ago
Better/more tests please
Updated 9 months ago1
Automatic testing with Carrot
Closed 9 months ago
FunctionalEquivalence: Improve binning for F1 plots
Closed 9 months ago1
Have TYPED_ONLY set for sites that are added back into imputed vcf
Closed 9 months ago1
The PRS "Wrapper"
Closed 9 months ago
Use gatk GatherVcfsCloud instead of picard GatherVcfs in Imputation pipeline
Closed 9 months ago1
Cleanup dockers in Imputation workflow
Closed 9 months ago1
FunctionalEquivalence: Add summary text to HTML report
Closed 2 years ago
Handle missing APOL1 CKD risk alleles correctly
Closed 2 years ago
Example inputs for FindSamplesAndBenchmark have the wrong picard jar
Closed 2 years ago1
Not specifying optional stratIntervals/stratLabels in FindSamplesAndBenchmark results in error.
Closed 2 years ago6
Truth data default "requester pays" buckets for FindSamplesAndBenchmark aren't accessible in Cromwell through Terra
Closed 2 years ago1
Keep sample names in output of FindSamplesAndBenchmark
Closed 3 years ago
BenchmarkVCFs fails sometimes for large input files
Closed 3 years ago
Check input sizes before running flashpca in scoring
Closed 3 years ago1
APOL1 recessive risk adjustment for CKD
Closed 3 years ago1
Ancestry dependent prs variance
Closed 3 years ago2