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Drop aggregation during report generation #868

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Drop aggregation during report generation

Drop aggregation during report generation #868

Triggered via pull request February 22, 2024 15:26
@nebfieldnebfield
synchronize #249
drop-report-aggregation
Status Failure
Total duration 8m 52s
Artifacts 1

ci.yml

on: pull_request
preload_docker  /  docker
3m 24s
preload_docker / docker
preload_singularity  /  singularity
2m 26s
preload_singularity / singularity
preload_ancestry  /  preload_reference
10s
preload_ancestry / preload_reference
Matrix: pytest_workflow_docker
Waiting for pending jobs
Matrix: standard_test_docker / docker
Waiting for pending jobs
Matrix: standard_test_docker / singularity
Waiting for pending jobs
Matrix: pytest_workflow_singularity
Matrix: standard_test_singularity / docker
Matrix: standard_test_singularity / singularity
ancestry_docker  /  docker
ancestry_docker / docker
ancestry_docker  /  singularity
ancestry_docker / singularity
ancestry_vcf_docker  /  docker
ancestry_vcf_docker / docker
ancestry_vcf_docker  /  singularity
ancestry_vcf_docker / singularity
ancestry_singularity  /  docker
0s
ancestry_singularity / docker
ancestry_singularity  /  singularity
5m 41s
ancestry_singularity / singularity
ancestry_vcf_singularity  /  docker
0s
ancestry_vcf_singularity / docker
ancestry_vcf_singularity  /  singularity
6m 7s
ancestry_vcf_singularity / singularity
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Annotations

3 errors and 32 warnings
preload_docker / docker
Process completed with exit code 123.
ancestry_singularity / singularity
Process completed with exit code 1.
ancestry_vcf_singularity / singularity
Process completed with exit code 1.
preload_ancestry / preload_reference
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/cache@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
preload_singularity / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/cache@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (plink2 vcf) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (plink2 testrelabelpvar) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (pgscatalog test bad accession) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (plink2 testrelabelbim) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test input check subworkflow) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test make compatible subworkflow with pfile) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (pgscatalog test good and bad accessions GRCh38) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (plink2 testmultiscore) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test match combine module) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
preload_docker / docker
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test match module) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (plink2 testsmallmultiscore) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (plink2 testscore) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test make compatible subworkflow with bfile) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test make compatible subworkflow with vcf) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test perfect apply score) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test input check subworkflow with liftover 38to37) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
standard_test_singularity / singularity (test, singularity, 22.10.0)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/setup-nextflow@v1, actions/cache@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test input check subworkflow with PGS catalog API and whitespace) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test input check subworkflow with PGS catalog API) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (pgscatalog test --pgs_id) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (plink2 testmultiscorefail) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test apply score subworkflow) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
standard_test_singularity / singularity (test, singularity, latest)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/setup-nextflow@v1, actions/cache@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (plink2 testsmallscore) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test input check subworkflow with liftover 37to38) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (pgscatalog test --efo_trait --pgp_id and --pgs_id) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
pytest_workflow_singularity (test combine scorefiles module) / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
ancestry_singularity / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/cache/restore@v3, actions/setup-python@v3, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
ancestry_vcf_singularity / singularity
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/cache/restore@v3, actions/setup-python@v3, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

Artifacts

Produced during runtime
Name Size
logs-singularity-ancestry Expired
2.69 GB