pgsc_calc v2.0.0-alpha.1 #749
smlmbrtci.yml
on: release
preload_docker
/
docker
3m 26s
preload_singularity
/
singularity
4m 24s
preload_ancestry
/
preload_reference
9m 31s
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
13s
ancestry_docker
/
singularity
0s
ancestry_singularity
/
docker
0s
ancestry_singularity
/
singularity
17s
Annotations
93 errors and 37 warnings
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pytest_workflow_docker (test input check subworkflow with PGS catalog API) / docker
Process completed with exit code 1.
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pytest_workflow_docker (plink2 testscore) / docker
Process completed with exit code 1.
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pytest_workflow_docker (plink2 vcf) / docker
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pytest_workflow_docker (plink2 testsmallmultiscore) / docker
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pytest_workflow_docker (test match combine module) / docker
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pytest_workflow_docker (test make compatible subworkflow with bfile) / docker
Process completed with exit code 1.
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pytest_workflow_docker (test input check subworkflow with PGS catalog API and whitespace) / docker
FailFast: cancelling since parallel instance has failed
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pytest_workflow_docker (test input check subworkflow with PGS catalog API and whitespace) / docker
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pytest_workflow_docker (test make compatible subworkflow with pfile) / docker
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standard_test_docker / docker (test, docker, latest)
Process completed with exit code 1.
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pytest_workflow_docker (test input check subworkflow with liftover 38to37) / docker
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pytest_workflow_docker (test input check subworkflow with liftover 38to37) / docker
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pytest_workflow_docker (plink2 testrelabelbim) / docker
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pytest_workflow_docker (test combine scorefiles module) / docker
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pytest_workflow_docker (plink2 testrelabelbim) / docker
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pytest_workflow_docker (test combine scorefiles module) / docker
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pytest_workflow_docker (test apply score subworkflow) / docker
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pytest_workflow_docker (test apply score subworkflow) / docker
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pytest_workflow_docker (test input check subworkflow) / docker
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pytest_workflow_docker (test input check subworkflow) / docker
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pytest_workflow_docker (plink2 testsmallscore) / docker
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pytest_workflow_docker (plink2 testsmallscore) / docker
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pytest_workflow_docker (test perfect apply score) / docker
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pytest_workflow_docker (test perfect apply score) / docker
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pytest_workflow_docker (plink2 testrelabelpvar) / docker
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pytest_workflow_docker (plink2 testrelabelpvar) / docker
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pytest_workflow_docker (test input check subworkflow with liftover 37to38) / docker
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pytest_workflow_docker (pgscatalog test --pgs_id) / docker
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pytest_workflow_docker (pgscatalog test --pgs_id) / docker
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pytest_workflow_docker (pgscatalog test --efo_trait --pgp_id and --pgs_id) / docker
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pytest_workflow_docker (pgscatalog test --efo_trait --pgp_id and --pgs_id) / docker
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standard_test_docker / docker (test, docker, 22.10.0)
Process completed with exit code 1.
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pytest_workflow_docker (pgscatalog test good and bad accessions GRCh38) / docker
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pytest_workflow_docker (pgscatalog test good and bad accessions GRCh38) / docker
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pytest_workflow_docker (test make compatible subworkflow with vcf) / docker
FailFast: cancelling since parallel instance has failed
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pytest_workflow_docker (plink2 testmultiscore) / docker
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pytest_workflow_docker (test make compatible subworkflow with vcf) / docker
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pytest_workflow_docker (plink2 testmultiscore) / docker
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pytest_workflow_docker (plink2 testmultiscorefail) / docker
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pytest_workflow_docker (test match module) / docker
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pytest_workflow_docker (plink2 testmultiscorefail) / docker
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pytest_workflow_docker (test match module) / docker
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pytest_workflow_docker (pgscatalog test bad accession) / docker
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pytest_workflow_docker (pgscatalog test bad accession) / docker
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pytest_workflow_singularity (plink2 vcf) / singularity
Cache service responded with 403
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pytest_workflow_singularity (plink2 testrelabelbim) / singularity
Cache service responded with 403
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standard_test_singularity / singularity (test, singularity, latest)
Process completed with exit code 1.
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pytest_workflow_singularity (test input check subworkflow) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (test input check subworkflow) / singularity
Cache service responded with 403
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pytest_workflow_singularity (test perfect apply score) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (test perfect apply score) / singularity
Cache service responded with 403
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pytest_workflow_singularity (plink2 testrelabelpvar) / singularity
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pytest_workflow_singularity (test input check subworkflow with PGS catalog API and whitespace) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (test input check subworkflow with PGS catalog API and whitespace) / singularity
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pytest_workflow_singularity (pgscatalog test good and bad accessions GRCh38) / singularity
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pytest_workflow_singularity (pgscatalog test good and bad accessions GRCh38) / singularity
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pytest_workflow_singularity (plink2 testsmallmultiscore) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (plink2 testsmallmultiscore) / singularity
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pytest_workflow_singularity (test input check subworkflow with liftover 38to37) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (test input check subworkflow with liftover 38to37) / singularity
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pytest_workflow_singularity (pgscatalog test bad accession) / singularity
Cache service responded with 403
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pytest_workflow_singularity (pgscatalog test --pgs_id) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (pgscatalog test --pgs_id) / singularity
The operation was canceled.
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pytest_workflow_singularity (pgscatalog test --efo_trait --pgp_id and --pgs_id) / singularity
Cache service responded with 403
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pytest_workflow_singularity (test apply score subworkflow) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (test apply score subworkflow) / singularity
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pytest_workflow_singularity (test match module) / singularity
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pytest_workflow_singularity (test match module) / singularity
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pytest_workflow_singularity (plink2 testscore) / singularity
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pytest_workflow_singularity (plink2 testscore) / singularity
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pytest_workflow_singularity (test match combine module) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (test match combine module) / singularity
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pytest_workflow_singularity (test make compatible subworkflow with bfile) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (test make compatible subworkflow with bfile) / singularity
The operation was canceled.
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pytest_workflow_singularity (test input check subworkflow with PGS catalog API) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (test input check subworkflow with PGS catalog API) / singularity
The operation was canceled.
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pytest_workflow_singularity (test make compatible subworkflow with pfile) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (test make compatible subworkflow with pfile) / singularity
The operation was canceled.
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pytest_workflow_singularity (plink2 testsmallscore) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (plink2 testsmallscore) / singularity
The operation was canceled.
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pytest_workflow_singularity (test input check subworkflow with liftover 37to38) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (test input check subworkflow with liftover 37to38) / singularity
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pytest_workflow_singularity (plink2 testmultiscore) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (plink2 testmultiscore) / singularity
The operation was canceled.
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pytest_workflow_singularity (test make compatible subworkflow with vcf) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (plink2 testmultiscorefail) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (test make compatible subworkflow with vcf) / singularity
The operation was canceled.
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pytest_workflow_singularity (plink2 testmultiscorefail) / singularity
The operation was canceled.
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pytest_workflow_singularity (test combine scorefiles module) / singularity
FailFast: cancelling since parallel instance has failed
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pytest_workflow_singularity (test combine scorefiles module) / singularity
The operation was canceled.
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standard_test_singularity / singularity (test, singularity, 22.10.0)
Process completed with exit code 1.
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ancestry_docker / docker
Process completed with exit code 1.
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ancestry_singularity / singularity
Cache service responded with 403
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pytest_workflow_docker (test input check subworkflow with PGS catalog API) / 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/
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pytest_workflow_docker (test input check subworkflow with PGS catalog API) / docker
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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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/
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pytest_workflow_docker (plink2 testscore) / docker
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_docker (plink2 vcf) / 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/
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pytest_workflow_docker (plink2 vcf) / docker
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_docker (plink2 testsmallmultiscore) / 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/
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pytest_workflow_docker (plink2 testsmallmultiscore) / docker
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_docker (test match combine module) / 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/
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pytest_workflow_docker (test match combine module) / docker
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_docker (test make compatible subworkflow with bfile) / 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/
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pytest_workflow_docker (test input check subworkflow with PGS catalog API and whitespace) / 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/
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pytest_workflow_docker (test make compatible subworkflow with bfile) / docker
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_docker (test input check subworkflow with PGS catalog API and whitespace) / docker
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_docker (test make compatible subworkflow with pfile) / 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/
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pytest_workflow_docker (test make compatible subworkflow with pfile) / docker
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_docker (test input check subworkflow with liftover 37to38) / 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/
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pytest_workflow_docker (test input check subworkflow with liftover 37to38) / docker
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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preload_singularity / singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: eWaterCycle/setup-singularity@v7. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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pytest_workflow_singularity (plink2 vcf) / 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/
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pytest_workflow_singularity (plink2 vcf) / singularity
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_singularity (plink2 testrelabelbim) / 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/
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pytest_workflow_singularity (plink2 testrelabelbim) / singularity
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_singularity (test input check subworkflow) / 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/
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pytest_workflow_singularity (test input check subworkflow) / singularity
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_singularity (test perfect apply score) / 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/
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pytest_workflow_singularity (test perfect apply score) / singularity
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_singularity (plink2 testrelabelpvar) / 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/
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pytest_workflow_singularity (plink2 testrelabelpvar) / singularity
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_singularity (pgscatalog test good and bad accessions GRCh38) / 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/
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pytest_workflow_singularity (pgscatalog test good and bad accessions GRCh38) / singularity
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_singularity (pgscatalog test bad accession) / 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/
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pytest_workflow_singularity (pgscatalog test bad accession) / singularity
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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pytest_workflow_singularity (pgscatalog test --efo_trait --pgp_id and --pgs_id) / 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/
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pytest_workflow_singularity (pgscatalog test --efo_trait --pgp_id and --pgs_id) / singularity
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity. No artifacts will be uploaded.
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ancestry_docker / docker
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/output/*. No artifacts will be uploaded.
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ancestry_singularity / singularity
No files were found with the provided path: /home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/output/*. No artifacts will be uploaded.
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