bump ALL gatk4 modules #17063
Triggered via pull request
November 13, 2024 13:45
matthdsm
Status
Cancelled
Total duration
5h 22m 9s
Artifacts
–
test.yml
on: pull_request
Matrix: nf-test
Matrix: nf-core-lint-modules
Matrix: nf-core-lint-modules
Matrix: pytest
confirm-pass
0s
Annotations
259 errors and 2 warnings
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nf-core-lint-modules (gatk4/applybqsr)
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nf-core-lint-modules (gatk4)
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nf-core-lint-modules (gatk4/annotateintervals)
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nf-core-lint-modules (gatk4/condensedepthevidence)
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nf-core-lint-modules (gatk4/applyvqsr)
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nf-core-lint-modules (gatk4/composestrtablefile)
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nf-core-lint-modules (gatk4/createsomaticpanelofnormals)
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nf-core-lint-modules (gatk4/genotypegvcfs)
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nf-core-lint-modules (gatk4/createreadcountpanelofnormals)
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nf-core-lint-modules (gatk4/calibratedragstrmodel)
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nf-core-lint-modules (gatk4/combinegvcfs)
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nf-core-lint-modules (gatk4/filtermutectcalls)
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nf-core-lint-modules (gatk4/gatherbqsrreports)
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nf-core-lint-modules (gatk4/createsequencedictionary)
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nf-core-lint-modules (gatk4/mergebamalignment)
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nf-core-lint-modules (gatk4/fastqtosam)
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nf-core-lint-modules (gatk4/splitcram)
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nf-core-lint-modules (gatk4/splitintervals)
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nf-core-lint-modules (gatk4spark/applybqsr)
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nf-test (modules/nf-core/gatk4/condensedepthevidence, conda)
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nf-test (modules/nf-core/gatk4/cnnscorevariants, singularity)
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nf-test (modules/nf-core/gatk4/samtofastq, singularity)
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nf-test (modules/nf-core/gatk4/collectreadcounts, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/combinegvcfs, conda)
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nf-test (modules/nf-core/gatk4/filterintervals, conda)
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nf-test (modules/nf-core/gatk4/determinegermlinecontigploidy, singularity)
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nf-test (modules/nf-core/gatk4/createsequencedictionary, conda)
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nf-test (modules/nf-core/gatk4/determinegermlinecontigploidy, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/filterintervals, singularity)
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nf-test (modules/nf-core/gatk4/filterintervals, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/germlinecnvcaller, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/genomicsdbimport, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/genomicsdbimport, singularity)
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nf-test (modules/nf-core/gatk4/germlinecnvcaller, singularity)
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nf-test (modules/nf-core/gatk4/intervallisttools, conda)
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nf-test (modules/nf-core/gatk4/germlinecnvcaller, conda)
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nf-test (modules/nf-core/gatk4/intervallisttools, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/learnreadorientationmodel, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/variantfiltration, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/learnreadorientationmodel, conda)
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nf-test (modules/nf-core/gatk4/variantfiltration, singularity)
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nf-test (modules/nf-core/gatk4/variantfiltration, conda)
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nf-test (modules/nf-core/gatk4/haplotypecaller, singularity)
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nf-test (modules/nf-core/gatk4/haplotypecaller, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/genomicsdbimport, conda)
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nf-test (modules/nf-core/gatk4/haplotypecaller, conda)
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nf-test (modules/nf-core/gatk4/indexfeaturefile, conda)
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nf-test (modules/nf-core/gatk4/indexfeaturefile, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/indexfeaturefile, singularity)
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nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, conda)
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nf-test (modules/nf-core/gatk4/mutect2, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, singularity)
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nf-test (modules/nf-core/gatk4/mergevcfs, conda)
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nf-test (modules/nf-core/gatk4/mergevcfs, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/mutect2, singularity)
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nf-test (modules/nf-core/gatk4/mutect2, conda)
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nf-test (modules/nf-core/gatk4/mergevcfs, singularity)
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nf-test (modules/nf-core/gatk4/printreads, singularity)
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nf-test (modules/nf-core/gatk4/printreads, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/printreads, conda)
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nf-test (modules/nf-core/gatk4/samtofastq, conda)
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nf-test (modules/nf-core/gatk4spark/baserecalibrator, conda)
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nf-test (modules/nf-core/gatk4spark/baserecalibrator, singularity)
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nf-test (modules/nf-core/gatk4spark/baserecalibrator, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/addorreplacereadgroups, docker_self_hosted)
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nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, docker_self_hosted)
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nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, singularity)
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nf-test (modules/nf-core/gatk4/addorreplacereadgroups, conda)
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nf-test (modules/nf-core/gatk4/addorreplacereadgroups, singularity)
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nf-test (modules/nf-core/gatk4/baserecalibrator, singularity)
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nf-test (modules/nf-core/gatk4/bedtointervallist, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/baserecalibrator, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/calculatecontamination, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/bedtointervallist, singularity)
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nf-test (modules/nf-core/gatk4/baserecalibrator, conda)
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nf-test (modules/nf-core/gatk4/bedtointervallist, conda)
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nf-test (modules/nf-core/gatk4/calculatecontamination, singularity)
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nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, conda)
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nf-test (modules/nf-core/gatk4/cnnscorevariants, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/denoisereadcounts, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/calculatecontamination, conda)
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nf-test (modules/nf-core/gatk4/denoisereadcounts, singularity)
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nf-test (modules/nf-core/gatk4/denoisereadcounts, conda)
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nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/filtervarianttranches, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/filtervarianttranches, singularity)
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nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, conda)
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nf-test (modules/nf-core/gatk4/filtervarianttranches, conda)
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nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, singularity)
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nf-test (modules/nf-core/gatk4/getpileupsummaries, singularity)
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nf-test (modules/nf-core/gatk4/getpileupsummaries, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/getpileupsummaries, conda)
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nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, singularity)
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nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, conda)
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nf-test (modules/nf-core/gatk4/reblockgvcf, conda)
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nf-test (modules/nf-core/gatk4/reblockgvcf, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/reblockgvcf, singularity)
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nf-test (modules/nf-core/gatk4/svannotate, singularity)
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nf-test (modules/nf-core/gatk4/splitintervals, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/selectvariants, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/splitintervals, singularity)
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nf-test (modules/nf-core/gatk4/collectsvevidence, docker_self_hosted)
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nf-test (modules/nf-core/gatk4/shiftfasta, singularity)
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nf-test (modules/nf-core/gatk4/selectvariants, singularity)
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nf-test (modules/nf-core/gatk4/collectsvevidence, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4/shiftfasta, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4/selectvariants, conda)
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nf-test (modules/nf-core/gatk4/collectsvevidence, singularity)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4/shiftfasta, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4spark/applybqsr, singularity)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4/splitintervals, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4spark/applybqsr, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4spark/applybqsr, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (subworkflows/nf-core/abundance_differential_filter, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (subworkflows/nf-core/abundance_differential_filter, singularity)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4/svannotate, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4/svannotate, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (subworkflows/nf-core/abundance_differential_filter, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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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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