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Add coptr module #17083

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Add coptr module

Add coptr module #17083

Triggered via pull request November 13, 2024 20:55
@ramirobarrantesramirobarrantes
synchronize #6935
coptr_map2
Status Failure
Total duration 18h 10m 12s
Artifacts –

test.yml

on: pull_request
nf-test-changes
1m 9s
nf-test-changes
pytest-changes
5s
pytest-changes
prettier
36s
prettier
editorconfig
16s
editorconfig
pre-commit
49s
pre-commit
Matrix: nf-test
Matrix: nf-core-lint-modules
Matrix: nf-core-lint-modules
Matrix: pytest
confirm-pass
2s
confirm-pass
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11 errors and 22 warnings
nf-core-lint-modules (coptr/map)
Process completed with exit code 1.
nf-test (modules/nf-core/coptr/map, docker_self_hosted)
Process completed with exit code 1.
nf-test (modules/nf-core/coptr/map, singularity)
Process completed with exit code 1.
nf-test (modules/nf-core/fgbio/collectduplexseqmetrics, docker_self_hosted)
The runner has received a shutdown signal. This can happen when the runner service is stopped, or a manually started runner is canceled.
nf-test (modules/nf-core/fgbio/collectduplexseqmetrics, docker_self_hosted)
The operation was canceled.
nf-test (modules/nf-core/coptr/map, conda)
Process completed with exit code 1.
nf-core-lint-modules (fgbio/callmolecularconsensusreads)
The self-hosted runner: ubuntu-2204-x64_i-01bcaa07f4b5ca684 lost communication with the server. Verify the machine is running and has a healthy network connection. Anything in your workflow that terminates the runner process, starves it for CPU/Memory, or blocks its network access can cause this error.
nf-test (modules/nf-core/fgbio/callduplexconsensusreads, docker_self_hosted)
The self-hosted runner: ubuntu-2204-x64_i-0f381e2fa942211df lost communication with the server. Verify the machine is running and has a healthy network connection. Anything in your workflow that terminates the runner process, starves it for CPU/Memory, or blocks its network access can cause this error.
nf-test (modules/nf-core/fgbio/callmolecularconsensusreads, docker_self_hosted)
The self-hosted runner: ubuntu-2204-x64_i-0756f04aecba2910d lost communication with the server. Verify the machine is running and has a healthy network connection. Anything in your workflow that terminates the runner process, starves it for CPU/Memory, or blocks its network access can cause this error.
nf-test (modules/nf-core/fgbio/callmolecularconsensusreads, singularity)
The self-hosted runner: ubuntu-2204-x64_i-0c2326eeba602e32b lost communication with the server. Verify the machine is running and has a healthy network connection. Anything in your workflow that terminates the runner process, starves it for CPU/Memory, or blocks its network access can cause this error.
confirm-pass
Process completed with exit code 1.
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.
nf-test (modules/nf-core/coptr/map, 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(
nf-test (modules/nf-core/coptr/map, conda)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
nf-test (modules/nf-core/fgbio/collectduplexseqmetrics, 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(
nf-test (modules/nf-core/fgbio/collectduplexseqmetrics, conda)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
nf-test (modules/nf-core/fgbio/callmolecularconsensusreads, 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(
nf-test (modules/nf-core/fgbio/callmolecularconsensusreads, conda)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
nf-test (modules/nf-core/fgbio/callduplexconsensusreads, 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(
nf-test (modules/nf-core/fgbio/callduplexconsensusreads, conda)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
nf-test (modules/nf-core/fgbio/filterconsensusreads, 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(
nf-test (modules/nf-core/fgbio/filterconsensusreads, conda)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
nf-test (modules/nf-core/fgbio/groupreadsbyumi, 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(
nf-test (modules/nf-core/fgbio/groupreadsbyumi, conda)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
nf-test (modules/nf-core/fgbio/sortbam, 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(
nf-test (modules/nf-core/fgbio/sortbam, conda)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
nf-test (modules/nf-core/fgbio/fastqtobam, 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(
nf-test (modules/nf-core/fgbio/fastqtobam, conda)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
nf-test (modules/nf-core/fgbio/zipperbams, 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(
nf-test (modules/nf-core/fgbio/zipperbams, conda)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
nf-test (subworkflows/nf-core/abundance_differential_filter, 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(
nf-test (subworkflows/nf-core/abundance_differential_filter, conda)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.