bump ALL gatk4 modules #16615
matthdsmtest.yml
on: pull_request
nf-test-changes
2m 40s
pytest-changes
8s
pre-commit
1m 31s
Matrix: nf-test
Matrix: nf-core-lint-modules
Matrix: nf-core-lint-modules
Matrix: pytest
confirm-pass
0s
Annotations
219 errors and 75 warnings
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pytest (gatk4/createreadcountpanelofnormals, singularity)
Process completed with exit code 1.
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pytest (gatk4/createreadcountpanelofnormals, singularity)
Process completed with exit code 1.
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pytest (gatk4/createreadcountpanelofnormals, conda)
Process completed with exit code 1.
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pytest (gatk4/createreadcountpanelofnormals, conda)
Process completed with exit code 1.
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pytest (gatk4/createsomaticpanelofnormals, conda)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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pytest (gatk4/createsomaticpanelofnormals, conda)
Process completed with exit code 1.
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pytest (gatk4/createsomaticpanelofnormals, conda)
Process completed with exit code 1.
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pytest (gatk4/intervallisttobed, conda)
EACCES: permission denied, scandir '/home/ubuntu/pytest_workflow_djdy61oo/gatk4_createsomaticpanelofnormals_test_gatk4_createsomaticpanelofnormals/work/4f/2d2430a3ac6421bf63e608fe612900/test_genomicsdb/chr22$1$40001'
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pytest (gatk4/intervallisttobed, conda)
Process completed with exit code 1.
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pytest (gatk4/intervallisttobed, conda)
Process completed with exit code 1.
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pytest (gatk4/filtervarianttranches, conda)
Process completed with exit code 1.
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pytest (gatk4/filtervarianttranches, conda)
Process completed with exit code 1.
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pytest (gatk4/filtervarianttranches, conda)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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pytest (gatk4/filtervarianttranches, singularity)
Process completed with exit code 1.
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pytest (gatk4/filtervarianttranches, singularity)
Process completed with exit code 1.
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pytest (gatk4/filtervarianttranches, singularity)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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pytest (gatk4/createsomaticpanelofnormals, singularity)
Process completed with exit code 1.
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pytest (gatk4/createsomaticpanelofnormals, singularity)
Process completed with exit code 1.
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pytest (gatk4/createsomaticpanelofnormals, singularity)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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pytest (gatk4/germlinecnvcaller, singularity)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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pytest (gatk4/germlinecnvcaller, singularity)
Process completed with exit code 1.
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pytest (gatk4/germlinecnvcaller, singularity)
Process completed with exit code 1.
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nf-core-lint-modules (gatk4)
Process completed with exit code 1.
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pytest (gatk4/sitedepthtobaf, conda)
Process completed with exit code 1.
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pytest (gatk4/sitedepthtobaf, conda)
Process completed with exit code 1.
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pytest (gatk4/sitedepthtobaf, conda)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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pytest (gatk4/printsvevidence, conda)
Process completed with exit code 1.
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pytest (gatk4/printsvevidence, conda)
Process completed with exit code 1.
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pytest (gatk4/printsvevidence, conda)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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pytest (gatk4/intervallisttobed, singularity)
Process completed with exit code 1.
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pytest (gatk4/intervallisttobed, singularity)
Process completed with exit code 1.
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pytest (gatk4/intervallisttobed, singularity)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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pytest (gatk4/printsvevidence, singularity)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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pytest (gatk4/printsvevidence, singularity)
Process completed with exit code 1.
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pytest (gatk4/printsvevidence, singularity)
Process completed with exit code 1.
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pytest (gatk4/sitedepthtobaf, singularity)
Process completed with exit code 1.
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pytest (gatk4/sitedepthtobaf, singularity)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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pytest (gatk4/sitedepthtobaf, singularity)
Process completed with exit code 1.
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nf-core-lint-modules (gatk4/mergevcfs)
Process completed with exit code 1.
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pytest (gatk4/variantrecalibrator, conda)
Process completed with exit code 1.
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pytest (gatk4/variantrecalibrator, conda)
Process completed with exit code 1.
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pytest (gatk4/variantrecalibrator, conda)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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pytest (gatk4/variantrecalibrator, singularity)
Process completed with exit code 1.
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pytest (gatk4/variantrecalibrator, singularity)
Process completed with exit code 1.
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pytest (gatk4/variantrecalibrator, singularity)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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nf-test (modules/nf-core/gatk4/mergemutectstats, singularity)
Process completed with exit code 1.
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nf-core-lint-modules (gatk4/splitintervals)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/bedtointervallist, conda)
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/gatk4/bedtointervallist, conda)
The operation was canceled.
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pytest (gatk4/germlinecnvcaller, docker)
Process completed with exit code 1.
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pytest (gatk4/germlinecnvcaller, docker)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/collectreadcounts, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/calculatecontamination, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/selectvariants, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/calibratedragstrmodel, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/splitncigarreads, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/createsequencedictionary, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/bedtointervallist, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/combinegvcfs, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/createsequencedictionary, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/getpileupsummaries, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/addorreplacereadgroups, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/splitintervals, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/mergevcfs, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/composestrtablefile, singularity)
Process completed with exit code 1.
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pytest (gatk4/determinegermlinecontigploidy, docker)
Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run
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pytest (gatk4/determinegermlinecontigploidy, docker)
Process completed with exit code 1.
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pytest (gatk4/determinegermlinecontigploidy, docker)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/gatherpileupsummaries, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/applyvqsr, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/mergevcfs, conda)
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/gatk4/mergevcfs, conda)
The operation was canceled.
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nf-test (modules/nf-core/gatk4/filterintervals, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/genotypegvcfs, 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/gatk4/genotypegvcfs, docker_self_hosted)
The operation was canceled.
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nf-test (modules/nf-core/gatk4/applybqsr, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/annotateintervals, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/baserecalibrator, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/bedtointervallist, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/gatherbqsrreports, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/combinegvcfs, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/denoisereadcounts, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/svannotate, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/calibratedragstrmodel, 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/gatk4/calibratedragstrmodel, docker_self_hosted)
The operation was canceled.
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nf-test (modules/nf-core/gatk4/splitncigarreads, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/composestrtablefile, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/gatherpileupsummaries, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/collectsvevidence, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/filtermutectcalls, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/splitintervals, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/collectreadcounts, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/getpileupsummaries, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/learnreadorientationmodel, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/fastqtosam, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/svannotate, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/indexfeaturefile, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/preprocessintervals, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/haplotypecaller, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/intervallisttools, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/learnreadorientationmodel, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/addorreplacereadgroups, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/applyvqsr, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/filterintervals, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/genomicsdbimport, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/indexfeaturefile, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/revertsam, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/shiftfasta, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/printreads, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/shiftfasta, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/printreads, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/gatherbqsrreports, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/preprocessintervals, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/calculatecontamination, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/fastqtosam, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/mergebamalignment, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/revertsam, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/splitcram, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/condensedepthevidence, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/denoisereadcounts, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/splitcram, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/baserecalibrator, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/intervallisttools, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/genotypegvcfs, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/svcluster, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/annotateintervals, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/samtofastq, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/reblockgvcf, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/variantstotable, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/mergebamalignment, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/filtermutectcalls, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/applybqsr, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/samtofastq, docker_self_hosted)
Process completed with exit code 1.
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nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/composestrtablefile, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/variantfiltration, singularity)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/svcluster, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/denoisereadcounts, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/mergemutectstats, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/haplotypecaller, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/collectsvevidence, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/reblockgvcf, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/genomicsdbimport, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/combinegvcfs, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/splitncigarreads, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/variantfiltration, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/condensedepthevidence, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/collectreadcounts, conda)
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/gatk4/collectreadcounts, conda)
The operation was canceled.
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nf-test (modules/nf-core/gatk4/splitintervals, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4, 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 (modules/nf-core/gatk4, singularity)
The operation was canceled.
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nf-test (modules/nf-core/gatk4/calculatecontamination, conda)
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/gatk4/calculatecontamination, conda)
The operation was canceled.
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nf-test (modules/nf-core/gatk4/intervallisttools, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/variantstotable, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/gatherpileupsummaries, conda)
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/gatk4/gatherpileupsummaries, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/gatherpileupsummaries, conda)
The operation was canceled.
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nf-test (modules/nf-core/gatk4/fastqtosam, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/applybqsr, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/filterintervals, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/createsequencedictionary, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/baserecalibrator, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/preprocessintervals, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/gatherbqsrreports, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/filtermutectcalls, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/learnreadorientationmodel, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/variantfiltration, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/revertsam, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/applyvqsr, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/calibratedragstrmodel, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/mergebamalignment, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/shiftfasta, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/splitcram, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/addorreplacereadgroups, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/variantstotable, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/mergemutectstats, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/annotateintervals, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/genomicsdbimport, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/svcluster, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/getpileupsummaries, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/haplotypecaller, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/samtofastq, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/printreads, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/indexfeaturefile, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/collectsvevidence, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/genotypegvcfs, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/svannotate, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/markduplicates, conda)
Process completed with exit code 1.
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nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, docker_self_hosted)
The operation was canceled.
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nf-test (modules/nf-core/gatk4/mutect2, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4/mutect2, docker_self_hosted)
The operation was canceled.
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nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, conda)
The operation was canceled.
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nf-test (modules/nf-core/gatk4, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4, docker_self_hosted)
The operation was canceled.
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nf-test (modules/nf-core/gatk4/mutect2, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4/mutect2, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/mutect2, conda)
The operation was canceled.
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nf-test (modules/nf-core/gatk4, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4, conda)
The operation was canceled.
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nf-test (modules/nf-core/gatk4, conda)
Process completed with exit code 1.
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nf-test (modules/nf-core/gatk4/mutect2, singularity)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4/mutect2, singularity)
The self-hosted runner: ubuntu-2204-x64_i-00a131ef3915aa756 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 (modules/nf-core/gatk4/condensedepthevidence, singularity)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4/condensedepthevidence, singularity)
The self-hosted runner: ubuntu-2204-x64_i-04fc7655145425908 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 (modules/nf-core/gatk4/markduplicates, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4/markduplicates, docker_self_hosted)
The self-hosted runner: ubuntu-2204-x64_i-06d399ece56fbb7d7 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 (modules/nf-core/gatk4/reblockgvcf, conda)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
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nf-test (modules/nf-core/gatk4/reblockgvcf, conda)
The self-hosted runner: ubuntu-2204-x64_i-00cdb2d88eca219c5 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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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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pytest (gatk4/createreadcountpanelofnormals, 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 (gatk4/createreadcountpanelofnormals, 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 (gatk4/createsomaticpanelofnormals, 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 (gatk4/createreadcountpanelofnormals, 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 (gatk4/createsomaticpanelofnormals, 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 (gatk4/intervallisttobed, 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 (gatk4/filtervarianttranches, 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 (gatk4/filtervarianttranches, 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 (gatk4/createsomaticpanelofnormals, 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 (gatk4/filtervarianttranches, 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 (gatk4/germlinecnvcaller, 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 (gatk4/sitedepthtobaf, 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 (gatk4/printsvevidence, 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 (gatk4/intervallisttobed, 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 (gatk4/printsvevidence, 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 (gatk4/sitedepthtobaf, 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 (gatk4/intervallisttobed, 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 (gatk4/variantrecalibrator, 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 (gatk4/variantrecalibrator, 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 (gatk4/sitedepthtobaf, 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 (gatk4/germlinecnvcaller, 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 (gatk4/printsvevidence, 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 (gatk4/variantrecalibrator, 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 (gatk4/determinegermlinecontigploidy, 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(
|
|
nf-test (modules/nf-core/gatk4/mergevcfs, 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(
|
|
nf-test (modules/nf-core/gatk4/composestrtablefile, 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(
|
|
nf-test (modules/nf-core/gatk4/denoisereadcounts, 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(
|
|
nf-test (modules/nf-core/gatk4/combinegvcfs, 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(
|
|
nf-test (modules/nf-core/gatk4/splitncigarreads, 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(
|
|
nf-test (modules/nf-core/gatk4/condensedepthevidence, 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(
|
|
nf-test (modules/nf-core/gatk4/collectreadcounts, 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(
|
|
nf-test (modules/nf-core/gatk4/splitintervals, 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(
|
|
nf-test (modules/nf-core/gatk4/calculatecontamination, 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(
|
|
nf-test (modules/nf-core/gatk4/intervallisttools, 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(
|
|
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, 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(
|
|
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, 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(
|
|
nf-test (modules/nf-core/gatk4/fastqtosam, 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(
|
|
nf-test (modules/nf-core/gatk4/applybqsr, 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(
|
|
nf-test (modules/nf-core/gatk4/filterintervals, 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(
|
|
nf-test (modules/nf-core/gatk4/createsequencedictionary, 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(
|
|
nf-test (modules/nf-core/gatk4/baserecalibrator, 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(
|
|
nf-test (modules/nf-core/gatk4/preprocessintervals, 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(
|
|
nf-test (modules/nf-core/gatk4/gatherbqsrreports, 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(
|
|
nf-test (modules/nf-core/gatk4/filtermutectcalls, 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(
|
|
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, 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(
|
|
nf-test (modules/nf-core/gatk4/variantfiltration, 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(
|
|
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, 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(
|
|
nf-test (modules/nf-core/gatk4/revertsam, 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(
|
|
nf-test (modules/nf-core/gatk4/applyvqsr, 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(
|
|
nf-test (modules/nf-core/gatk4/selectvariants, 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(
|
|
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, 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(
|
|
nf-test (modules/nf-core/gatk4/mergebamalignment, 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(
|
|
nf-test (modules/nf-core/gatk4/shiftfasta, 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(
|
|
nf-test (modules/nf-core/gatk4/splitcram, 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(
|
|
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, 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(
|
|
nf-test (modules/nf-core/gatk4/variantstotable, 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(
|
|
nf-test (modules/nf-core/gatk4/mergemutectstats, 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(
|
|
nf-test (modules/nf-core/gatk4/annotateintervals, 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(
|
|
nf-test (modules/nf-core/gatk4/genomicsdbimport, 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(
|
|
nf-test (subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka, 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(
|
|
nf-test (modules/nf-core/gatk4/svcluster, 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(
|
|
nf-test (modules/nf-core/gatk4/getpileupsummaries, 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(
|
|
nf-test (modules/nf-core/gatk4/haplotypecaller, 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(
|
|
nf-test (modules/nf-core/gatk4/samtofastq, 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(
|
|
nf-test (modules/nf-core/gatk4/printreads, 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(
|
|
nf-test (modules/nf-core/gatk4/indexfeaturefile, 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(
|
|
nf-test (modules/nf-core/gatk4/collectsvevidence, 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(
|
|
nf-test (modules/nf-core/gatk4/genotypegvcfs, 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(
|
|
nf-test (modules/nf-core/gatk4/svannotate, 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(
|
|
nf-test (modules/nf-core/gatk4/markduplicates, 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(
|
|
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, 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(
|
|
nf-test (modules/nf-core/gatk4/mutect2, 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(
|
|
nf-test (modules/nf-core/gatk4, 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(
|
Artifacts
Produced during runtime
| Name | Size | |
|---|---|---|
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logs-conda-
|
28.4 KB |
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logs-docker-
|
1.56 MB |
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logs-singularity-
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28.5 KB |
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