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bump ALL gatk4 modules #16619

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bump ALL gatk4 modules

bump ALL gatk4 modules #16619

Triggered via pull request October 31, 2024 10:46
@matthdsmmatthdsm
synchronize #6917
matthdsm:bump/gatk
Status Cancelled
Total duration 2m 42s
Artifacts –

test.yml

on: pull_request
nf-test-changes
1m 11s
nf-test-changes
pytest-changes
4s
pytest-changes
prettier
31s
prettier
editorconfig
17s
editorconfig
pre-commit
49s
pre-commit
Matrix: nf-test
Matrix: nf-core-lint-modules
Matrix: nf-core-lint-modules
Matrix: pytest
confirm-pass
0s
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50 errors and 16 warnings
pytest (gatk4/filtervarianttranches, singularity)
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pytest (gatk4/filtervarianttranches, singularity)
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pytest (gatk4/createsomaticpanelofnormals, singularity)
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pytest (gatk4/createsomaticpanelofnormals, singularity)
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pytest (gatk4/determinegermlinecontigploidy, docker)
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pytest (gatk4/determinegermlinecontigploidy, docker)
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pytest (gatk4/intervallisttobed, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/filtervarianttranches, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/intervallisttobed, conda)
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pytest (gatk4/filtervarianttranches, conda)
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pytest (gatk4/variantrecalibrator, conda)
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pytest (gatk4/variantrecalibrator, conda)
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pytest (gatk4/sitedepthtobaf, singularity)
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pytest (gatk4/sitedepthtobaf, singularity)
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pytest (gatk4/createreadcountpanelofnormals, docker)
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pytest (gatk4/createreadcountpanelofnormals, docker)
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pytest (gatk4/createsomaticpanelofnormals, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/createsomaticpanelofnormals, docker)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/createsomaticpanelofnormals, conda)
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pytest (gatk4/createsomaticpanelofnormals, docker)
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pytest (gatk4/sitedepthtobaf, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/sitedepthtobaf, conda)
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pytest (gatk4/printsvevidence, docker)
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pytest (gatk4/printsvevidence, docker)
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pytest (gatk4/germlinecnvcaller, singularity)
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pytest (gatk4/germlinecnvcaller, singularity)
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pytest (gatk4/variantrecalibrator, singularity)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/variantrecalibrator, singularity)
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pytest (gatk4/printsvevidence, singularity)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/printsvevidence, singularity)
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pytest (gatk4/intervallisttobed, singularity)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/intervallisttobed, singularity)
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pytest (gatk4/germlinecnvcaller, docker)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/germlinecnvcaller, docker)
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pytest (gatk4/filtervarianttranches, docker)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/filtervarianttranches, docker)
The operation was canceled.
pytest (gatk4/createreadcountpanelofnormals, singularity)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/createreadcountpanelofnormals, singularity)
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pytest (gatk4/sitedepthtobaf, docker)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/sitedepthtobaf, docker)
The operation was canceled.
pytest (gatk4/variantrecalibrator, docker)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/variantrecalibrator, docker)
The operation was canceled.
pytest (gatk4/printsvevidence, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/printsvevidence, conda)
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nf-test-changes
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nf-test-changes
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pytest (gatk4/intervallisttobed, docker)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/intervallisttobed, docker)
The operation was canceled.
pytest (gatk4/createreadcountpanelofnormals, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
pytest (gatk4/createreadcountpanelofnormals, conda)
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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/
pre-commit
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
pytest (gatk4/createsomaticpanelofnormals, singularity)
/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(
pytest (gatk4/determinegermlinecontigploidy, docker)
/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(
pytest (gatk4/intervallisttobed, 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(
pytest (gatk4/filtervarianttranches, 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(
pytest (gatk4/variantrecalibrator, 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(
pytest (gatk4/sitedepthtobaf, singularity)
/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(
pytest (gatk4/createreadcountpanelofnormals, docker)
/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(
pytest (gatk4/createsomaticpanelofnormals, docker)
/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(
pytest (gatk4/printsvevidence, singularity)
/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(
pytest (gatk4/intervallisttobed, singularity)
/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(
pytest (gatk4/germlinecnvcaller, docker)
/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(
pytest (gatk4/sitedepthtobaf, docker)
/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(
pytest (gatk4/intervallisttobed, docker)
/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(
pytest (gatk4/createreadcountpanelofnormals, 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(