Add nf-test to vcf_annotation_ensemblvep_snpeff + some general fixes #15985
nvnieuwktest.yml
on: pull_request
Matrix: nf-test
Matrix: nf-core-lint-modules
Matrix: nf-core-lint-modules
Matrix: pytest
confirm-pass
4s
Annotations
12 errors and 2 warnings
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nf-core-lint-modules (vcf_annotate_ensemblvep_snpeff)
Process completed with exit code 1.
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nf-test (modules/nf-core/bismark/coverage2cytosine, 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.
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nf-test (modules/nf-core/bismark/coverage2cytosine, docker_self_hosted)
The operation was canceled.
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nf-test (subworkflows/nf-core/fastq_fastqc_umitools_trimgalore, singularity)
The runner has received a shutdown signal. This can happen when the runner service is stopped, or a manually started runner is canceled.
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nf-test (subworkflows/nf-core/fastq_fastqc_umitools_trimgalore, singularity)
The operation was canceled.
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nf-test (subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness, singularity)
The runner has received a shutdown signal. This can happen when the runner service is stopped, or a manually started runner is canceled.
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nf-test (subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness, singularity)
The operation was canceled.
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nf-test (subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff, singularity)
Process completed with exit code 1.
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nf-test (subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff, docker_self_hosted)
Process completed with exit code 1.
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nf-test (subworkflows/nf-core/fastq_fastqc_umitools_fastp, docker_self_hosted)
The self-hosted runner: ubuntu-2204-x64_i-07918c807be55eba1 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.
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nf-test (subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff, conda)
Process completed with exit code 1.
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confirm-pass
Process completed with exit code 1.
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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/
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pre-commit
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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