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add --error-on-freq-calc to improve scoring efficiency #716

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add --error-on-freq-calc to improve scoring efficiency

add --error-on-freq-calc to improve scoring efficiency #716

Run time

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Job Run time
preload_ancestry / preload_reference
16s
preload_docker / docker
3m 47s
preload_singularity / singularity
2m 7s
ancestry_singularity / docker
0s
standard_test_singularity / docker
0s
ancestry_singularity / singularity
7m 41s
standard_test_singularity / singularity (test, singularity, 22.10.0)
1m 32s
standard_test_singularity / singularity (test, singularity, latest)
1m 7s
pytest_workflow_singularity (pgscatalog test bad accession) / singularity
57s
pytest_workflow_singularity (pgscatalog test bad accession) / docker
0s
pytest_workflow_singularity (pgscatalog test --efo_trait --pgp_id and --pgs_id) / docker
0s
pytest_workflow_singularity (pgscatalog test --efo_trait --pgp_id and --pgs_id) / singularity
2m 2s
pytest_workflow_singularity (pgscatalog test good and bad accessions GRCh38) / docker
0s
pytest_workflow_singularity (pgscatalog test good and bad accessions GRCh38) / singularity
1m 10s
pytest_workflow_singularity (pgscatalog test --pgs_id) / singularity
47s
pytest_workflow_singularity (pgscatalog test --pgs_id) / docker
0s
pytest_workflow_singularity (plink2 testmultiscore) / docker
0s
pytest_workflow_singularity (plink2 testmultiscore) / singularity
1m 11s
pytest_workflow_singularity (plink2 testmultiscorefail) / docker
0s
pytest_workflow_singularity (plink2 testrelabelbim) / docker
0s
pytest_workflow_singularity (plink2 testrelabelpvar) / docker
0s
pytest_workflow_singularity (plink2 testmultiscorefail) / singularity
52s
pytest_workflow_singularity (plink2 testrelabelpvar) / singularity
1m 9s
pytest_workflow_singularity (plink2 testrelabelbim) / singularity
1m 37s
pytest_workflow_singularity (plink2 testscore) / docker
0s
pytest_workflow_singularity (plink2 testscore) / singularity
57s
pytest_workflow_singularity (plink2 testsmallmultiscore) / docker
0s
pytest_workflow_singularity (plink2 testsmallmultiscore) / singularity
1m 4s
pytest_workflow_singularity (plink2 testsmallscore) / docker
0s
pytest_workflow_singularity (plink2 testsmallscore) / singularity
1m 22s
pytest_workflow_singularity (plink2 vcf) / docker
0s
pytest_workflow_singularity (plink2 vcf) / singularity
59s
pytest_workflow_singularity (test apply score subworkflow) / docker
0s
pytest_workflow_singularity (test apply score subworkflow) / singularity
1m 29s
pytest_workflow_singularity (test combine scorefiles module) / docker
0s
pytest_workflow_singularity (test combine scorefiles module) / singularity
2m 18s
pytest_workflow_singularity (test input check subworkflow) / docker
0s
pytest_workflow_singularity (test input check subworkflow) / singularity
54s
pytest_workflow_singularity (test input check subworkflow with liftover 37to38) / docker
0s
pytest_workflow_singularity (test input check subworkflow with liftover 37to38) / singularity
1m 10s
pytest_workflow_singularity (test input check subworkflow with liftover 38to37) / docker
0s
pytest_workflow_singularity (test input check subworkflow with liftover 38to37) / singularity
1m 29s
pytest_workflow_singularity (test input check subworkflow with PGS catalog API) / docker
0s
pytest_workflow_singularity (test input check subworkflow with PGS catalog API) / singularity
1m 10s
pytest_workflow_singularity (test input check subworkflow with PGS catalog API and whitespace) / docker
0s
pytest_workflow_singularity (test input check subworkflow with PGS catalog API and whitespace) / singularity
1m 14s
pytest_workflow_singularity (test make compatible subworkflow with bfile) / docker
0s
pytest_workflow_singularity (test make compatible subworkflow with bfile) / singularity
1m 12s
pytest_workflow_singularity (test make compatible subworkflow with pfile) / docker
0s
pytest_workflow_singularity (test make compatible subworkflow with pfile) / singularity
55s
pytest_workflow_singularity (test make compatible subworkflow with vcf) / docker
0s
pytest_workflow_singularity (test make compatible subworkflow with vcf) / singularity
1m 8s
pytest_workflow_singularity (test match combine module) / docker
0s
pytest_workflow_singularity (test match combine module) / singularity
1m 0s
pytest_workflow_singularity (test match module) / docker
0s
pytest_workflow_singularity (test match module) / singularity
56s
pytest_workflow_singularity (test perfect apply score) / singularity
1m 21s
pytest_workflow_singularity (test perfect apply score) / docker
0s
ancestry_docker / docker
7m 47s
ancestry_docker / singularity
0s
standard_test_docker / docker (test, docker, 22.10.0)
1m 54s
standard_test_docker / docker (test, docker, latest)
1m 55s
standard_test_docker / singularity
0s
pytest_workflow_docker (pgscatalog test bad accession) / docker
2m 1s
pytest_workflow_docker (pgscatalog test bad accession) / singularity
0s
pytest_workflow_docker (pgscatalog test --efo_trait --pgp_id and --pgs_id) / docker
2m 49s
pytest_workflow_docker (pgscatalog test --efo_trait --pgp_id and --pgs_id) / singularity
0s
pytest_workflow_docker (pgscatalog test good and bad accessions GRCh38) / docker
1m 41s
pytest_workflow_docker (pgscatalog test good and bad accessions GRCh38) / singularity
0s
pytest_workflow_docker (pgscatalog test --pgs_id) / docker
1m 42s
pytest_workflow_docker (pgscatalog test --pgs_id) / singularity
0s
pytest_workflow_docker (plink2 testmultiscore) / docker
1m 44s
pytest_workflow_docker (plink2 testmultiscore) / singularity
0s
pytest_workflow_docker (plink2 testmultiscorefail) / docker
1m 59s
pytest_workflow_docker (plink2 testmultiscorefail) / singularity
0s
pytest_workflow_docker (plink2 testrelabelbim) / docker
1m 43s
pytest_workflow_docker (plink2 testrelabelbim) / singularity
0s
pytest_workflow_docker (plink2 testrelabelpvar) / docker
2m 19s
pytest_workflow_docker (plink2 testrelabelpvar) / singularity
0s
pytest_workflow_docker (plink2 testscore) / docker
1m 47s
pytest_workflow_docker (plink2 testscore) / singularity
0s
pytest_workflow_docker (plink2 testsmallmultiscore) / docker
2m 4s
pytest_workflow_docker (plink2 testsmallscore) / docker
1m 59s
pytest_workflow_docker (plink2 testsmallmultiscore) / singularity
0s
pytest_workflow_docker (plink2 testsmallscore) / singularity
0s
pytest_workflow_docker (plink2 vcf) / docker
2m 10s
pytest_workflow_docker (plink2 vcf) / singularity
0s
pytest_workflow_docker (test apply score subworkflow) / docker
1m 59s
pytest_workflow_docker (test apply score subworkflow) / singularity
0s
pytest_workflow_docker (test combine scorefiles module) / docker
3m 9s
pytest_workflow_docker (test input check subworkflow) / docker
2m 15s
pytest_workflow_docker (test combine scorefiles module) / singularity
0s
pytest_workflow_docker (test input check subworkflow) / singularity
0s
pytest_workflow_docker (test input check subworkflow with liftover 37to38) / docker
2m 32s
pytest_workflow_docker (test input check subworkflow with liftover 37to38) / singularity
0s
pytest_workflow_docker (test input check subworkflow with liftover 38to37) / docker
1m 53s
pytest_workflow_docker (test input check subworkflow with liftover 38to37) / singularity
0s
pytest_workflow_docker (test input check subworkflow with PGS catalog API) / docker
1m 53s
pytest_workflow_docker (test input check subworkflow with PGS catalog API) / singularity
0s
pytest_workflow_docker (test input check subworkflow with PGS catalog API and whitespace) / docker
1m 56s
pytest_workflow_docker (test input check subworkflow with PGS catalog API and whitespace) / singularity
0s
pytest_workflow_docker (test make compatible subworkflow with bfile) / docker
2m 15s
pytest_workflow_docker (test make compatible subworkflow with bfile) / singularity
0s
pytest_workflow_docker (test make compatible subworkflow with pfile) / docker
2m 17s
pytest_workflow_docker (test make compatible subworkflow with pfile) / singularity
0s
pytest_workflow_docker (test make compatible subworkflow with vcf) / docker
2m 17s
pytest_workflow_docker (test make compatible subworkflow with vcf) / singularity
0s
pytest_workflow_docker (test match combine module) / docker
2m 4s
pytest_workflow_docker (test match module) / docker
1m 57s
pytest_workflow_docker (test match combine module) / singularity
0s
pytest_workflow_docker (test match module) / singularity
0s
pytest_workflow_docker (test perfect apply score) / docker
2m 4s
pytest_workflow_docker (test perfect apply score) / singularity
0s
1h 50m 58s