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Add nf-test to vcf_annotation_ensemblvep_snpeff + some general fixes #15984

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Add nf-test to vcf_annotation_ensemblvep_snpeff + some general fixes

Add nf-test to vcf_annotation_ensemblvep_snpeff + some general fixes #15984

Triggered via pull request October 17, 2024 15:22
@nvnieuwknvnieuwk
synchronize #6779
nvnieuwk:update-annotation-subwf
Status Cancelled
Total duration 12m 56s
Artifacts –

test.yml

on: pull_request
nf-test-changes
2m 13s
nf-test-changes
pytest-changes
8s
pytest-changes
prettier
32s
prettier
editorconfig
12s
editorconfig
pre-commit
44s
pre-commit
Matrix: nf-test
Matrix: nf-core-lint-modules
Matrix: nf-core-lint-modules
Matrix: pytest
confirm-pass
0s
confirm-pass
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65 errors and 2 warnings
nf-core-lint-modules (vcf_annotate_ensemblvep_snpeff)
Process completed with exit code 1.
nf-test (modules/nf-core/arriba/download, 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/arriba/download, docker_self_hosted)
The operation was canceled.
nf-test (modules/nf-core/arriba/download, singularity)
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/arriba/download, singularity)
The operation was canceled.
nf-test (modules/nf-core/bismark/genomepreparation, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/bismark/deduplicate, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/svdb/merge, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/fastq_fastqc_umitools_fastp, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/fastq_fastqc_umitools_fastp, conda)
The operation was canceled.
nf-test (modules/nf-core/bismark/summary, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/bismark/summary, conda)
The operation was canceled.
nf-test (modules/nf-core/bismark/align, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/bismark/align, docker_self_hosted)
The operation was canceled.
nf-test (modules/nf-core/samshee, singularity)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/samshee, singularity)
The operation was canceled.
nf-test (modules/nf-core/proovframe/map, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/proovframe/map, conda)
The operation was canceled.
nf-test (subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff, conda)
The operation was canceled.
nf-test (subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness, singularity)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness, singularity)
The operation was canceled.
nf-test (subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff, docker_self_hosted)
The operation was canceled.
nf-test (subworkflows/nf-core/fastq_fastqc_umitools_fastp, singularity)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/fastq_fastqc_umitools_fastp, singularity)
The operation was canceled.
nf-test (subworkflows/nf-core/fastq_fastqc_umitools_fastp, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/fastq_fastqc_umitools_fastp, docker_self_hosted)
The operation was canceled.
nf-test (subworkflows/nf-core/fastq_fastqc_umitools_trimgalore, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/fastq_fastqc_umitools_trimgalore, docker_self_hosted)
The operation was canceled.
nf-test (subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff, singularity)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff, singularity)
The operation was canceled.
nf-test (subworkflows/nf-core/fastq_fastqc_umitools_trimgalore, singularity)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/fastq_fastqc_umitools_trimgalore, singularity)
The operation was canceled.
nf-test (subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness, docker_self_hosted)
The operation was canceled.
nf-test (modules/nf-core/arriba/arriba, singularity)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/arriba/arriba, singularity)
The operation was canceled.
nf-test (modules/nf-core/samshee, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/samshee, conda)
The operation was canceled.
nf-test (subworkflows/nf-core/fastq_fastqc_umitools_trimgalore, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/fastq_fastqc_umitools_trimgalore, conda)
The operation was canceled.
nf-test (modules/nf-core/deepvariant/vcfstatsreport, singularity)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/deepvariant/vcfstatsreport, singularity)
The operation was canceled.
nf-test (modules/nf-core/bismark/align, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/bismark/align, conda)
The operation was canceled.
nf-test (modules/nf-core/svdb/merge, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/svdb/merge, conda)
The operation was canceled.
nf-test (modules/nf-core/bwameth/align, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/bwameth/align, conda)
The operation was canceled.
nf-test (modules/nf-core/deepvariant/vcfstatsreport, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/deepvariant/vcfstatsreport, docker_self_hosted)
The operation was canceled.
nf-test (subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness, conda)
The operation was canceled.
nf-test (modules/nf-core/bismark/coverage2cytosine, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/bismark/coverage2cytosine, conda)
The operation was canceled.
nf-test (modules/nf-core/bismark/report, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/bismark/report, conda)
The operation was canceled.
nf-test (modules/nf-core/arriba/download, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/arriba/download, conda)
Process completed with exit code 1.
nf-test (modules/nf-core/arriba/download, conda)
The operation was canceled.
nf-test (modules/nf-core/arriba/arriba, conda)
Canceling since a higher priority waiting request for 'Run tests-6779' exists
nf-test (modules/nf-core/arriba/arriba, conda)
Process completed with exit code 1.
nf-test (modules/nf-core/arriba/arriba, conda)
The operation was canceled.
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.