Parabricks haplotypecaller version update and tests migrated to nf-test #17249
Triggered via pull request
November 15, 2024 12:33
Furentsu
Status
Failure
Total duration
21m 12s
Artifacts
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test.yml
on: pull_request
Matrix: nf-test
Matrix: nf-test with GPUs
Matrix: nf-core-lint-modules
Matrix: nf-core-lint-modules
Matrix: pytest
confirm-pass
2s
Annotations
8 errors and 3 warnings
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nf-core-lint-modules (parabricks/haplotypecaller)
Process completed with exit code 1.
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confirm-pass
Process completed with exit code 1.
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nf-test with GPUs (modules/nf-core/parabricks/haplotypecaller, docker_self_hosted)
Process completed with exit code 1.
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nf-test with GPUs (modules/nf-core/parabricks/applybqsr)
Process completed with exit code 2.
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nf-test with GPUs (modules/nf-core/parabricks/haplotypecaller, singularity)
Process completed with exit code 1.
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nf-test with GPUs (modules/nf-core/parabricks/fq2bam)
Process completed with exit code 1.
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nf-test with GPUs (modules/nf-core/parabricks/fq2bammeth)
Process completed with exit code 1.
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nf-test with GPUs (modules/nf-core/parabricks/haplotypecaller, conda)
Process completed with exit code 1.
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pytest-changes
The following actions use a deprecated Node.js version and will be forced to run on node20: mirpedrol/paths-filter@main. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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pre-commit
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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nf-test with GPUs (modules/nf-core/parabricks/haplotypecaller, conda)
/home/ubuntu/miniconda3/lib/python3.12/site-packages/conda/base/context.py:198: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:
conda config --add channels defaults
For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html
deprecated.topic(
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