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add crabs/dbimport from readsimulator pipeline #17395

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add crabs/dbimport from readsimulator pipeline

add crabs/dbimport from readsimulator pipeline #17395

Triggered via pull request November 18, 2024 13:26
@famosabfamosab
synchronize #6584
famosab:crabs-2
Status Cancelled
Total duration 1m 41s
Artifacts –

test.yml

on: pull_request
nf-test-changes
1m 20s
nf-test-changes
pytest-changes
4s
pytest-changes
prettier
31s
prettier
editorconfig
13s
editorconfig
pre-commit
52s
pre-commit
Matrix: nf-test-gpu
Matrix: nf-test
Matrix: nf-core-lint-modules
Matrix: nf-core-lint-modules
Matrix: pytest
confirm-pass
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20 errors and 9 warnings
pytest (subworkflows/utils_nextflow_pipeline, singularity)
Canceling since a higher priority waiting request for 'Run tests-6584' exists
pytest (subworkflows/utils_nextflow_pipeline, singularity)
The operation was canceled.
pytest (cooler/balance, singularity)
Canceling since a higher priority waiting request for 'Run tests-6584' exists
pytest (cooler/balance, singularity)
The operation was canceled.
pytest (cooler/balance, conda)
Canceling since a higher priority waiting request for 'Run tests-6584' exists
pytest (cooler/balance, conda)
The operation was canceled.
pytest (subworkflows/utils_nextflow_pipeline, docker)
Canceling since a higher priority waiting request for 'Run tests-6584' exists
pytest (subworkflows/utils_nextflow_pipeline, docker)
The operation was canceled.
pytest (subworkflows/utils_nextflow_pipeline, conda)
Canceling since a higher priority waiting request for 'Run tests-6584' exists
pytest (subworkflows/utils_nextflow_pipeline, conda)
The operation was canceled.
nf-test-changes
Canceling since a higher priority waiting request for 'Run tests-6584' exists
nf-test-changes
The operation was canceled.
pytest (gatk4/determinegermlinecontigploidy, docker)
Canceling since a higher priority waiting request for 'Run tests-6584' exists
pytest (gatk4/determinegermlinecontigploidy, docker)
The operation was canceled.
pytest (cooler/balance, docker)
Canceling since a higher priority waiting request for 'Run tests-6584' exists
pytest (cooler/balance, docker)
The operation was canceled.
pytest (gatk4/germlinecnvcaller, singularity)
Canceling since a higher priority waiting request for 'Run tests-6584' exists
pytest (gatk4/germlinecnvcaller, singularity)
The operation was canceled.
pytest (gatk4/germlinecnvcaller, docker)
Canceling since a higher priority waiting request for 'Run tests-6584' exists
pytest (gatk4/germlinecnvcaller, docker)
The operation was canceled.
pytest (subworkflows/utils_nextflow_pipeline, singularity)
/home/runner/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 (cooler/balance, singularity)
/home/runner/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 (cooler/balance, conda)
/home/runner/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 (subworkflows/utils_nextflow_pipeline, docker)
/home/runner/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 (subworkflows/utils_nextflow_pipeline, conda)
/home/runner/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/runner/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 (cooler/balance, docker)
/home/runner/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, singularity)
/home/runner/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/runner/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(