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New module: Kraken2/Bracken on Unaligned Sequences for Contamination Detection #2974

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New module: Kraken2/Bracken on Unaligned Sequences for Contamination Detection

New module: Kraken2/Bracken on Unaligned Sequences for Contamination Detection #2974

Triggered via pull request September 19, 2024 16:07
@egreenberg7egreenberg7
opened #1388
egreenberg7:dev
Status Cancelled
Total duration 8m 33s
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68 errors and 56 warnings
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
modules/nf-core/kraken2/kraken2/tests/main.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
modules/nf-core/kraken2/kraken2/tests/main.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
modules/nf-core/bracken/bracken/tests/main.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
modules/nf-core/bracken/bracken/tests/main.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
modules/nf-core/hisat2/align/tests/main.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
modules/nf-core/hisat2/align/tests/main.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
subworkflows/local/align_star/tests/main.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
subworkflows/local/align_star/tests/main.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/salmon.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/salmon.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/kallisto.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/kallisto.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/skip_qc.nf.test docker NF-latest-everything
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/skip_qc.nf.test docker NF-latest-everything
The operation was canceled.
tests/skip_qc.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/featurecounts_group_type.nf.test docker NF-latest-everything
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/featurecounts_group_type.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/featurecounts_group_type.nf.test docker NF-latest-everything
The operation was canceled.
tests/remove_ribo_rna.nf.test docker NF-23.04
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/remove_ribo_rna.nf.test docker NF-23.04
The operation was canceled.
tests/remove_ribo_rna.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/star_rsem.nf.test docker NF-latest-everything
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/star_rsem.nf.test docker NF-latest-everything
The operation was canceled.
tests/star_rsem.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/default.nf.test docker NF-latest-everything
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/default.nf.test docker NF-latest-everything
The operation was canceled.
tests/default.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/skip_trimming.nf.test docker NF-latest-everything
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/skip_trimming.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/skip_trimming.nf.test docker NF-latest-everything
The operation was canceled.
tests/min_mapped_reads.nf.test docker NF-23.04
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/min_mapped_reads.nf.test docker NF-23.04
The operation was canceled.
tests/min_mapped_reads.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/hisat2.nf.test docker NF-23.04
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/hisat2.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/hisat2.nf.test docker NF-23.04
The operation was canceled.
tests/default.nf.test docker NF-23.04
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/default.nf.test docker NF-23.04
The operation was canceled.
tests/default.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/remove_ribo_rna.nf.test docker NF-latest-everything
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/remove_ribo_rna.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/remove_ribo_rna.nf.test docker NF-latest-everything
The operation was canceled.
tests/featurecounts_group_type.nf.test docker NF-23.04
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/featurecounts_group_type.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/featurecounts_group_type.nf.test docker NF-23.04
The operation was canceled.
tests/min_mapped_reads.nf.test docker NF-latest-everything
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/min_mapped_reads.nf.test docker NF-latest-everything
The operation was canceled.
tests/min_mapped_reads.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/skip_qc.nf.test docker NF-23.04
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/skip_qc.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/skip_qc.nf.test docker NF-23.04
The operation was canceled.
tests/skip_trimming.nf.test docker NF-23.04
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/skip_trimming.nf.test docker NF-23.04
The operation was canceled.
tests/skip_trimming.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/star_rsem.nf.test docker NF-23.04
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/star_rsem.nf.test docker NF-23.04
The operation was canceled.
tests/star_rsem.nf.test docker NF-23.04
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/hisat2.nf.test docker NF-latest-everything
Canceling since a higher priority waiting request for 'nf-core CI-1388' exists
tests/hisat2.nf.test docker NF-latest-everything
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
tests/hisat2.nf.test docker NF-latest-everything
The operation was canceled.
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test docker NF-latest-everything
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test docker NF-23.04
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test docker NF-latest-everything
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
modules/nf-core/kraken2/kraken2/tests/main.nf.test docker NF-23.04
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
modules/nf-core/kraken2/kraken2/tests/main.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
modules/nf-core/kraken2/kraken2/tests/main.nf.test docker NF-latest-everything
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
modules/nf-core/kraken2/kraken2/tests/main.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
modules/nf-core/bracken/bracken/tests/main.nf.test docker NF-23.04
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
modules/nf-core/bracken/bracken/tests/main.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
modules/nf-core/bracken/bracken/tests/main.nf.test docker NF-latest-everything
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
modules/nf-core/bracken/bracken/tests/main.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test docker NF-latest-everything
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test docker NF-23.04
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
modules/nf-core/hisat2/align/tests/main.nf.test docker NF-latest-everything
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
modules/nf-core/hisat2/align/tests/main.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
modules/nf-core/hisat2/align/tests/main.nf.test docker NF-23.04
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
modules/nf-core/hisat2/align/tests/main.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test docker NF-23.04
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
subworkflows/local/align_star/tests/main.nf.test docker NF-23.04
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
subworkflows/local/align_star/tests/main.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
subworkflows/local/align_star/tests/main.nf.test docker NF-latest-everything
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
subworkflows/local/align_star/tests/main.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test docker NF-latest-everything
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test docker NF-23.04
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/salmon.nf.test docker NF-23.04
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
tests/salmon.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/salmon.nf.test docker NF-latest-everything
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
tests/salmon.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/kallisto.nf.test docker NF-23.04
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
tests/kallisto.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/kallisto.nf.test docker NF-latest-everything
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
tests/kallisto.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/skip_qc.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/featurecounts_group_type.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/remove_ribo_rna.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/star_rsem.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/default.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/skip_trimming.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/min_mapped_reads.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/hisat2.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/default.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/remove_ribo_rna.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/featurecounts_group_type.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/min_mapped_reads.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/skip_qc.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/skip_trimming.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/star_rsem.nf.test docker NF-23.04
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
tests/hisat2.nf.test docker NF-latest-everything
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23