Fix minor typos #19302
mribeirodantasAnnotations
103 errors and 50 warnings
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pytest (subworkflows/fastq_create_umi_consensus_fgbio, conda)
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pytest (subworkflows/fastq_create_umi_consensus_fgbio, conda)
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pytest (subworkflows/vcf_annotate_ensemblvep, conda)
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pytest (subworkflows/vcf_annotate_ensemblvep, conda)
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pytest (subworkflows/vcf_annotate_ensemblvep, singularity)
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pytest (subworkflows/vcf_annotate_ensemblvep, singularity)
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pytest (universc, docker)
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pytest (subworkflows/fastq_create_umi_consensus_fgbio, docker)
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pytest (subworkflows/fastq_create_umi_consensus_fgbio, docker)
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pytest (subworkflows/fastq_align_bwaaln, singularity)
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pytest (subworkflows/fastq_align_bwaaln, singularity)
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pytest (subworkflows/fastq_align_bwaaln, conda)
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pytest (subworkflows/fastq_align_bwaaln, conda)
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pytest (subworkflows/bam_cnv_wisecondorx, docker)
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pytest (subworkflows/bam_cnv_wisecondorx, docker)
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pytest (subworkflows/fastq_create_umi_consensus_fgbio, singularity)
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pytest (subworkflows/fastq_create_umi_consensus_fgbio, singularity)
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pytest (subworkflows/bam_cnv_wisecondorx, conda)
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pytest (subworkflows/bam_cnv_wisecondorx, conda)
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pytest (subworkflows/vcf_annotate_ensemblvep, docker)
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pytest (subworkflows/vcf_annotate_ensemblvep, docker)
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pytest (sgdemux, docker)
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pytest (sgdemux, docker)
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pytest (subworkflows/bam_cnv_wisecondorx, singularity)
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pytest (subworkflows/bam_cnv_wisecondorx, singularity)
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pytest (sgdemux, singularity)
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pytest (sgdemux, singularity)
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pytest (cooler/balance, singularity)
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pytest (cooler/balance, singularity)
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pytest (propr/logratio, singularity)
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pytest (duphold, singularity)
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pytest (graphtyper/genotype, conda)
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pytest (duphold, singularity)
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pytest (graphtyper/genotype, conda)
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pytest (subworkflows/bam_tumor_only_somatic_variant_calling_gatk, docker)
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pytest (subworkflows/bam_tumor_only_somatic_variant_calling_gatk, docker)
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pytest (custom/matrixfilter, singularity)
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pytest (custom/matrixfilter, singularity)
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pytest (duphold, conda)
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pytest (duphold, conda)
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pytest (duphold, docker)
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pytest (duphold, docker)
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pytest (graphtyper/genotype, docker)
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pytest (graphtyper/genotype, docker)
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pytest (graphtyper/genotype, singularity)
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pytest (graphtyper/genotype, singularity)
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pytest (ivar/consensus, conda)
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pytest (ivar/consensus, conda)
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pytest (hmmer/eslreformat, docker)
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pytest (hmmer/eslreformat, docker)
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pytest (mmseqs/easysearch, conda)
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pytest (mmseqs/easysearch, conda)
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pytest (msisensor/msi, conda)
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pytest (msisensor/msi, conda)
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pytest (propr/logratio, conda)
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pytest (propr/logratio, conda)
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pytest (msisensor/msi, docker)
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pytest (msisensor/msi, docker)
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pytest (sgdemux, conda)
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pytest (sgdemux, conda)
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pytest (hmmer/eslreformat, conda)
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pytest (hmmer/eslreformat, conda)
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pytest (ivar/consensus, singularity)
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pytest (ivar/consensus, singularity)
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pytest (mmseqs/easysearch, docker)
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pytest (mmseqs/easysearch, docker)
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pytest (parabricks/mutectcaller, docker)
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pytest (parabricks/mutectcaller, docker)
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pytest (hmmer/eslreformat, singularity)
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pytest (hmmer/eslreformat, singularity)
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pytest (propr/logratio, docker)
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pytest (msisensor/msi, singularity)
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pytest (msisensor/msi, singularity)
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pytest (parabricks/mutectcaller, singularity)
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pytest (parabricks/mutectcaller, singularity)
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pytest (mmseqs/easysearch, singularity)
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pytest (mmseqs/easysearch, singularity)
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pytest (ivar/consensus, docker)
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pytest (ivar/consensus, docker)
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pytest (subworkflows/fastq_align_bwaaln, docker)
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pytest (subworkflows/fastq_align_bwaaln, docker)
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pytest (subworkflows/bam_tumor_only_somatic_variant_calling_gatk, conda)
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pytest (subworkflows/bam_tumor_only_somatic_variant_calling_gatk, conda)
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pytest (subworkflows/bam_tumor_only_somatic_variant_calling_gatk, singularity)
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pytest (subworkflows/bam_tumor_only_somatic_variant_calling_gatk, singularity)
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pytest (bbmap/align, conda)
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pytest (bbmap/align, conda)
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pytest (coreograph, docker)
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pytest (cooler/balance, docker)
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pytest (coreograph, docker)
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pytest (cooler/balance, docker)
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pytest (custom/matrixfilter, docker)
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pytest (custom/matrixfilter, docker)
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pytest (custom/matrixfilter, conda)
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pytest (custom/matrixfilter, conda)
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pytest (cooler/balance, conda)
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pytest (cooler/balance, conda)
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pytest (bbmap/align, singularity)
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pytest (bbmap/align, singularity)
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pytest (coreograph, singularity)
Canceling since a higher priority waiting request for 'Run pytest-workflow-7177' exists
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pytest (coreograph, singularity)
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pytest (bbmap/align, docker)
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pytest (bbmap/align, docker)
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pytest-changes
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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pytest (cooler/balance, 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(
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pytest (cooler/balance, singularity)
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'.
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pytest (duphold, 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(
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pytest (duphold, singularity)
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'.
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pytest (graphtyper/genotype, 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(
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pytest (graphtyper/genotype, 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'.
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pytest (custom/matrixfilter, 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(
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pytest (custom/matrixfilter, singularity)
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'.
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pytest (duphold, 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(
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pytest (duphold, 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'.
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pytest (duphold, 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(
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pytest (duphold, docker)
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'.
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pytest (graphtyper/genotype, 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(
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pytest (graphtyper/genotype, docker)
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'.
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pytest (graphtyper/genotype, 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(
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pytest (graphtyper/genotype, singularity)
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'.
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pytest (ivar/consensus, 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(
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pytest (ivar/consensus, 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'.
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pytest (hmmer/eslreformat, 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(
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pytest (hmmer/eslreformat, docker)
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'.
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pytest (mmseqs/easysearch, 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(
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pytest (mmseqs/easysearch, 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'.
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pytest (hmmer/eslreformat, 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(
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pytest (hmmer/eslreformat, 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'.
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pytest (ivar/consensus, 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(
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pytest (ivar/consensus, singularity)
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'.
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pytest (hmmer/eslreformat, 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(
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pytest (hmmer/eslreformat, singularity)
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'.
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pytest (ivar/consensus, 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(
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pytest (ivar/consensus, docker)
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'.
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pytest (bbmap/align, 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(
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pytest (bbmap/align, 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'.
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pytest (cooler/balance, 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(
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pytest (coreograph, 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 (cooler/balance, docker)
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'.
|
|
pytest (coreograph, docker)
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'.
|
|
pytest (custom/matrixfilter, 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 (custom/matrixfilter, docker)
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'.
|
|
pytest (custom/matrixfilter, 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 (custom/matrixfilter, 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'.
|
|
pytest (cooler/balance, 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 (cooler/balance, 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'.
|
|
pytest (bbmap/align, 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 (bbmap/align, singularity)
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'.
|
|
pytest (coreograph, 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 (coreograph, singularity)
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'.
|
|
pytest (bbmap/align, 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 (bbmap/align, docker)
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'.
|
|
confirm-pass
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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