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Update Docs and Fix a bug on the onCompleteMerging #565

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Update Docs and Fix a bug on the onCompleteMerging

Update Docs and Fix a bug on the onCompleteMerging #565

Triggered via pull request February 7, 2025 11:05
@luisasluisas
opened #192
luisas:docs
Status Cancelled
Total duration 2m 19s
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ci.yml

on: pull_request
Matrix: Stub run
Matrix: test
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60 errors and 20 warnings
Stub run (latest-everything, singularity, --skip_validation, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, docker, --skip_stats, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, singularity, --skip_compression, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, singularity, --skip_visualisation, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, singularity, --skip_preprocessing, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, singularity, --skip_stats, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, singularity, --skip_shiny, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, conda, --skip_stats, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, singularity, --skip_eval, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, docker, --skip_validation, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, conda, --skip_eval, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (24.04.2 | test_nosheet | conda)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, conda, --skip_stats, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (latest-everything | test_nosheet | conda)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, conda, --skip_validation, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, singularity, --skip_compression, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, conda, --skip_shiny, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (24.04.2 | test | conda)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, conda, --skip_preprocessing, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, docker, --skip_shiny, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, docker, --skip_shiny, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, conda, --skip_eval, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, conda, --skip_compression, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, docker, --skip_compression, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (latest-everything | test_pdb | singularity)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, docker, --skip_eval, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, docker, --skip_eval, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, docker, --skip_preprocessing, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, docker, --skip_validation, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (latest-everything | test | singularity)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, singularity, --skip_stats, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, conda, --skip_shiny, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, conda, --skip_visualisation, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, docker, --skip_stats, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (latest-everything | test | conda)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (24.04.2 | test_nosheet | singularity)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (latest-everything | test_pdb | conda)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (latest-everything | test_pdb | docker)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, singularity, --skip_eval, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, singularity, --skip_visualisation, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, conda, --skip_visualisation, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, docker, --skip_compression, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (24.04.2 | test_pdb | docker)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (latest-everything | test | docker)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, singularity, --skip_preprocessing, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, docker, --skip_visualisation, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, singularity, --skip_shiny, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (24.04.2 | test_pdb | conda)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, conda, --skip_preprocessing, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (latest-everything, docker, --skip_visualisation, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (24.04.2 | test | docker)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (24.04.2 | test | singularity)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (24.04.2 | test_pdb | singularity)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, conda, --skip_validation, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, conda, --skip_compression, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, docker, --skip_preprocessing, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (latest-everything | test_nosheet | singularity)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (latest-everything | test_nosheet | docker)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, singularity, --skip_validation, test, true)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Run pipeline with test data (24.04.2 | test_nosheet | docker)
Canceling since a higher priority waiting request for 'nf-core CI-192' exists
Stub run (24.04.2, conda, --skip_stats, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (latest-everything, conda, --skip_eval, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Run pipeline with test data (24.04.2 | test_nosheet | conda)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (latest-everything, conda, --skip_stats, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Run pipeline with test data (latest-everything | test_nosheet | conda)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (latest-everything, conda, --skip_validation, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (latest-everything, conda, --skip_shiny, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Run pipeline with test data (24.04.2 | test | conda)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (24.04.2, conda, --skip_preprocessing, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (24.04.2, conda, --skip_eval, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (latest-everything, conda, --skip_compression, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (24.04.2, conda, --skip_shiny, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (24.04.2, conda, --skip_visualisation, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Run pipeline with test data (latest-everything | test | conda)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Run pipeline with test data (latest-everything | test_pdb | conda)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (latest-everything, conda, --skip_visualisation, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Run pipeline with test data (24.04.2 | test_pdb | conda)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (latest-everything, conda, --skip_preprocessing, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (24.04.2, conda, --skip_validation, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(
Stub run (24.04.2, conda, --skip_compression, test, true)
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:202: 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(