Fix plink2_score options #780

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Triggered via pull request September 27, 2023 16:40

smlmbrt

synchronize #181

check_freqcalc

Status Cancelled

Total duration 12m 20s

Artifacts 2

ci.yml

on: pull_request

preload_docker / docker

preload_singularity / singularity

preload_ancestry / preload_reference

Matrix: pytest_workflow_docker

Matrix: standard_test_docker / docker

Matrix: standard_test_docker / singularity

Matrix: pytest_workflow_singularity

Matrix: standard_test_singularity / docker

Matrix: standard_test_singularity / singularity

ancestry_docker / docker

ancestry_docker / singularity

ancestry_vcf_docker / docker

ancestry_vcf_docker / singularity

ancestry_singularity / docker

ancestry_singularity / singularity

ancestry_vcf_singularity / docker

ancestry_vcf_singularity / singularity

Annotations

74 errors and 3 warnings

pytest_workflow_singularity (plink2 testmultiscore) / singularity

Process completed with exit code 1.

pytest_workflow_singularity (test match combine module) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test match combine module) / singularity

The operation was canceled.

pytest_workflow_singularity (test match module) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test match module) / singularity

The operation was canceled.

pytest_workflow_singularity (plink2 vcf) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (plink2 vcf) / singularity

The operation was canceled.

pytest_workflow_singularity (plink2 testrelabelpvar) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (plink2 testrelabelpvar) / singularity

The operation was canceled.

pytest_workflow_singularity (test input check subworkflow) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test input check subworkflow) / singularity

The operation was canceled.

pytest_workflow_singularity (test make compatible subworkflow with bfile) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test make compatible subworkflow with bfile) / singularity

The operation was canceled.

pytest_workflow_singularity (pgscatalog test bad accession) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (pgscatalog test bad accession) / singularity

The operation was canceled.

pytest_workflow_singularity (plink2 testsmallscore) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (plink2 testsmallscore) / singularity

The operation was canceled.

pytest_workflow_singularity (test input check subworkflow with liftover 38to37) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test input check subworkflow with liftover 38to37) / singularity

The operation was canceled.

pytest_workflow_singularity (pgscatalog test --pgs_id) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (pgscatalog test --pgs_id) / singularity

The operation was canceled.

pytest_workflow_singularity (plink2 testmultiscorefail) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (plink2 testscore) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (plink2 testmultiscorefail) / singularity

The operation was canceled.

pytest_workflow_singularity (plink2 testscore) / singularity

The operation was canceled.

pytest_workflow_singularity (test make compatible subworkflow with vcf) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test make compatible subworkflow with vcf) / singularity

The operation was canceled.

pytest_workflow_singularity (test input check subworkflow with liftover 37to38) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test input check subworkflow with liftover 37to38) / singularity

The operation was canceled.

pytest_workflow_singularity (test apply score subworkflow) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test apply score subworkflow) / singularity

The operation was canceled.

pytest_workflow_singularity (test perfect apply score) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test perfect apply score) / singularity

The operation was canceled.

pytest_workflow_singularity (test input check subworkflow with PGS catalog API and whitespace) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test input check subworkflow with PGS catalog API and whitespace) / singularity

The operation was canceled.

pytest_workflow_singularity (plink2 testrelabelbim) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (plink2 testrelabelbim) / singularity

The operation was canceled.

pytest_workflow_singularity (test input check subworkflow with PGS catalog API) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test make compatible subworkflow with pfile) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test input check subworkflow with PGS catalog API) / singularity

The operation was canceled.

pytest_workflow_singularity (test make compatible subworkflow with pfile) / singularity

The operation was canceled.

pytest_workflow_singularity (test combine scorefiles module) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (pgscatalog test good and bad accessions GRCh38) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (test combine scorefiles module) / singularity

The operation was canceled.

pytest_workflow_singularity (pgscatalog test good and bad accessions GRCh38) / singularity

The operation was canceled.

pytest_workflow_singularity (pgscatalog test --efo_trait --pgp_id and --pgs_id) / singularity

FailFast: cancelling since parallel instance has failed

pytest_workflow_singularity (pgscatalog test --efo_trait --pgp_id and --pgs_id) / singularity

The operation was canceled.

pytest_workflow_docker (plink2 testscore) / docker

Process completed with exit code 1.

pytest_workflow_docker (pgscatalog test bad accession) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (test input check subworkflow with liftover 38to37) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (test input check subworkflow) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (test make compatible subworkflow with bfile) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (test make compatible subworkflow with bfile) / docker

The operation was canceled.

pytest_workflow_docker (plink2 testmultiscorefail) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (plink2 testmultiscorefail) / docker

The operation was canceled.

pytest_workflow_docker (test input check subworkflow with PGS catalog API and whitespace) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (test input check subworkflow with PGS catalog API and whitespace) / docker

The operation was canceled.

pytest_workflow_docker (plink2 testsmallscore) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (plink2 testsmallscore) / docker

The operation was canceled.

pytest_workflow_docker (pgscatalog test --efo_trait --pgp_id and --pgs_id) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (pgscatalog test --efo_trait --pgp_id and --pgs_id) / docker

The operation was canceled.

pytest_workflow_docker (test input check subworkflow with liftover 37to38) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (test input check subworkflow with liftover 37to38) / docker

The operation was canceled.

pytest_workflow_docker (test input check subworkflow with PGS catalog API) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (test input check subworkflow with PGS catalog API) / docker

The operation was canceled.

pytest_workflow_docker (test combine scorefiles module) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (test combine scorefiles module) / docker

The operation was canceled.

pytest_workflow_docker (test make compatible subworkflow with pfile) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (test make compatible subworkflow with pfile) / docker

The operation was canceled.

pytest_workflow_docker (test match module) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (plink2 testmultiscore) / docker

The operation was canceled.

pytest_workflow_docker (plink2 testmultiscore) / docker

Process completed with exit code 1.

pytest_workflow_docker (test apply score subworkflow) / docker

FailFast: cancelling since parallel instance has failed

pytest_workflow_docker (test apply score subworkflow) / docker

The operation was canceled.

pytest_workflow_singularity (plink2 testmultiscore) / singularity

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

pytest_workflow_docker (plink2 testscore) / docker

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

pytest_workflow_docker (plink2 testmultiscore) / docker

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

Artifacts

Produced during runtime

Name	Size
logs-docker-plink2 testscore Expired	2.56 MB
logs-singularity-plink2 testmultiscore Expired	2.63 MB