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add crabs/insilicopcr module from readsimulator #17396

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add crabs/insilicopcr module from readsimulator

add crabs/insilicopcr module from readsimulator #17396

Triggered via pull request November 18, 2024 13:27
@famosabfamosab
synchronize #6583
famosab:crabs-1
Status Cancelled
Total duration 1m 27s
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test.yml

on: pull_request
nf-test-changes
1m 10s
nf-test-changes
pytest-changes
12s
pytest-changes
prettier
32s
prettier
editorconfig
11s
editorconfig
pre-commit
59s
pre-commit
Matrix: nf-test-gpu
Matrix: nf-test
Matrix: nf-core-lint-modules
Matrix: nf-core-lint-modules
Matrix: pytest
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21 errors and 9 warnings
pre-commit
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pytest (cooler/balance, singularity)
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pytest (cooler/balance, singularity)
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pytest (gatk4/germlinecnvcaller, singularity)
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pytest (gatk4/germlinecnvcaller, singularity)
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pytest (subworkflows/utils_nextflow_pipeline, docker)
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pytest (subworkflows/utils_nextflow_pipeline, docker)
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pytest (gatk4/germlinecnvcaller, docker)
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pytest (gatk4/germlinecnvcaller, docker)
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pytest (subworkflows/utils_nextflow_pipeline, singularity)
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pytest (subworkflows/utils_nextflow_pipeline, singularity)
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pytest (cooler/balance, docker)
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pytest (cooler/balance, docker)
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pytest (gatk4/determinegermlinecontigploidy, docker)
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pytest (gatk4/determinegermlinecontigploidy, docker)
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pytest (subworkflows/utils_nextflow_pipeline, conda)
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pytest (subworkflows/utils_nextflow_pipeline, conda)
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pytest (cooler/balance, conda)
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pytest (cooler/balance, conda)
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nf-test-changes
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nf-test-changes
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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 (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 (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 (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(
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, 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/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 (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 (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(