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bump ALL gatk4 modules #17363

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bump ALL gatk4 modules

bump ALL gatk4 modules #17363

Re-run triggered November 18, 2024 13:01
@matthdsmmatthdsm
#6917
matthdsm:bump/gatk
Status Cancelled
Total duration 48m 50s
Artifacts –

test.yml

on: pull_request
nf-test-changes
5m 28s
nf-test-changes
pytest-changes
7s
pytest-changes
prettier
29s
prettier
editorconfig
13s
editorconfig
pre-commit
36s
pre-commit
Matrix: nf-test-gpu
Matrix: nf-test
Matrix: nf-core-lint-modules
Matrix: nf-core-lint-modules
Matrix: pytest
confirm-pass
0s
confirm-pass
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21 errors and 255 warnings
nf-core-lint-modules (gatk4)
Process completed with exit code 1.
nf-test (modules/nf-core/gatk4, conda)
The runner has received a shutdown signal. This can happen when the runner service is stopped, or a manually started runner is canceled.
nf-test (modules/nf-core/gatk4, conda)
The operation was canceled.
nf-test (modules/nf-core/gatk4/genomicsdbimport, docker_self_hosted)
Process completed with exit code 1.
nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, conda)
Process completed with exit code 1.
nf-test (modules/nf-core/gatk4spark/baserecalibrator, docker_self_hosted)
Process completed with exit code 1.
nf-test (modules/nf-core/gatk4/germlinecnvcaller, conda)
Process completed with exit code 1.
nf-test (modules/nf-core/gatk4spark/applybqsr, docker_self_hosted)
Process completed with exit code 1.
nf-test (modules/nf-core/gatk4/markduplicates, conda)
Process completed with exit code 1.
nf-test (modules/nf-core/gatk4/createreadcountpanelofnormals, docker_self_hosted)
Process completed with exit code 1.
nf-test (modules/nf-core/gatk4spark/markduplicates, docker_self_hosted)
The self-hosted runner: ubuntu-2204-x64_i-0e0560c142103d50a 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.
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, docker_self_hosted)
Process completed with exit code 1.
nf-test (modules/nf-core/gatk4/germlinecnvcaller, docker_self_hosted)
Process completed with exit code 1.
nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, docker_self_hosted)
Process completed with exit code 1.
nf-test (modules/nf-core/gatk4/mutect2, conda)
The runner has received a shutdown signal. This can happen when the runner service is stopped, or a manually started runner is canceled.
nf-test (modules/nf-core/gatk4/mutect2, conda)
The operation was canceled.
nf-test (modules/nf-core/gatk4/mutect2, singularity)
Process completed with exit code 1.
nf-test (modules/nf-core/gatk4/mutect2, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
nf-test (modules/nf-core/gatk4, singularity)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
nf-test (modules/nf-core/gatk4, docker_self_hosted)
Canceling since a higher priority waiting request for 'Run tests-6917' exists
confirm-pass
Process completed with exit code 1.
nf-core-lint-modules (gatk4/mergebamalignment)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/variantfiltration)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/collectreadcounts)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/denoisereadcounts)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/preprocessintervals)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/samtofastq)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/markduplicates)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/intervallisttools)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/genotypegvcfs)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/learnreadorientationmodel)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/calibratedragstrmodel)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/splitncigarreads)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/genomicsdbimport)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/annotateintervals)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/sitedepthtobaf)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/addorreplacereadgroups)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/printsvevidence)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/intervallisttobed)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/svcluster)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/haplotypecaller)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/reblockgvcf)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/gatherpileupsummaries)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/mergevcfs)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/filtermutectcalls)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/gatherbqsrreports)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/applybqsr)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/bedtointervallist)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/determinegermlinecontigploidy)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/leftalignandtrimvariants)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/applyvqsr)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/condensedepthevidence)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/cnnscorevariants)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/createsequencedictionary)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/filterintervals)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/splitcram)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/printreads)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/shiftfasta)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/splitintervals)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/filtervarianttranches)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4spark/baserecalibrator)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/baserecalibrator)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/revertsam)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/mergemutectstats)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/postprocessgermlinecnvcalls)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/mutect2)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/indexfeaturefile)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/composestrtablefile)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4spark/markduplicates)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/createreadcountpanelofnormals)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4spark/applybqsr)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/germlinecnvcaller)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/combinegvcfs)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/fastqtosam)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/collectsvevidence)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/svannotate)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/getpileupsummaries)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/createsomaticpanelofnormals)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/selectvariants)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/variantrecalibrator)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/estimatelibrarycomplexity)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-core-lint-modules (gatk4/variantstotable)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-test (modules/nf-core/gatk4/mergebamalignment, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/mergebamalignment, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-core-lint-modules (gatk4/calculatecontamination)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-test (modules/nf-core/gatk4/mergebamalignment, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/variantfiltration, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/variantfiltration, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/variantfiltration, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/collectreadcounts, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/collectreadcounts, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/collectreadcounts, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/preprocessintervals, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/preprocessintervals, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/denoisereadcounts, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/denoisereadcounts, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/denoisereadcounts, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/preprocessintervals, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/samtofastq, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/samtofastq, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/samtofastq, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/intervallisttools, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/markduplicates, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/markduplicates, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/intervallisttools, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/intervallisttools, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/genotypegvcfs, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/genotypegvcfs, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/genotypegvcfs, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/splitncigarreads, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/splitncigarreads, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/splitncigarreads, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/annotateintervals, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/genomicsdbimport, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/annotateintervals, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/genomicsdbimport, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/sitedepthtobaf, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/sitedepthtobaf, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/sitedepthtobaf, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/printsvevidence, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/printsvevidence, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/intervallisttobed, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/printsvevidence, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/intervallisttobed, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/intervallisttobed, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/svcluster, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/svcluster, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/svcluster, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/haplotypecaller, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/haplotypecaller, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/mergevcfs, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/haplotypecaller, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/reblockgvcf, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/reblockgvcf, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/reblockgvcf, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/filtermutectcalls, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/filtermutectcalls, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/gatherbqsrreports, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/gatherbqsrreports, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/applybqsr, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/gatherbqsrreports, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/applybqsr, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/bedtointervallist, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/bedtointervallist, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/bedtointervallist, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/condensedepthevidence, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/condensedepthevidence, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/condensedepthevidence, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/applyvqsr, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/applyvqsr, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/applyvqsr, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/cnnscorevariants, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/cnnscorevariants, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/createsequencedictionary, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/createsequencedictionary, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/createsequencedictionary, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/filterintervals, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/filterintervals, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/splitcram, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/splitcram, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/splitcram, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/printreads, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/shiftfasta, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/printreads, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/shiftfasta, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/splitintervals, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/shiftfasta, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/splitintervals, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/filtervarianttranches, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/splitintervals, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/filtervarianttranches, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/filtervarianttranches, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/baserecalibrator, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/baserecalibrator, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/baserecalibrator, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4spark/baserecalibrator, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4spark/baserecalibrator, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/revertsam, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/revertsam, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/revertsam, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/mergemutectstats, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/mergemutectstats, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/mergemutectstats, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/indexfeaturefile, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/composestrtablefile, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/indexfeaturefile, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/composestrtablefile, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4spark/markduplicates, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/composestrtablefile, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4spark/markduplicates, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/createreadcountpanelofnormals, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4spark/applybqsr, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4spark/applybqsr, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/combinegvcfs, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/combinegvcfs, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/combinegvcfs, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/fastqtosam, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/fastqtosam, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/fastqtosam, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/collectsvevidence, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/svannotate, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/collectsvevidence, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/svannotate, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/collectsvevidence, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/svannotate, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/createsomaticpanelofnormals, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/createsomaticpanelofnormals, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/getpileupsummaries, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/getpileupsummaries, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/createsomaticpanelofnormals, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/selectvariants, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/selectvariants, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/selectvariants, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/variantrecalibrator, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/variantrecalibrator, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/variantrecalibrator, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/variantstotable, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/calculatecontamination, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/variantstotable, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/variantstotable, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/calculatecontamination, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/calculatecontamination, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-core-lint-modules (gatk4)
Failed to restore: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
nf-test (modules/nf-core/gatk4, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/genomicsdbimport, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/filtermutectcalls, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4spark/baserecalibrator, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/germlinecnvcaller, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/indexfeaturefile, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/mergevcfs, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4spark/applybqsr, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/markduplicates, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/filterintervals, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/createreadcountpanelofnormals, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/mergevcfs, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/printreads, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/determinegermlinecontigploidy, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/getpileupsummaries, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/createreadcountpanelofnormals, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/applybqsr, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/determinegermlinecontigploidy, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/annotateintervals, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/germlinecnvcaller, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/germlinecnvcaller, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/mutect2, conda)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/mutect2, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4/mutect2, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4, singularity)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
nf-test (modules/nf-core/gatk4, docker_self_hosted)
The `python-version` input is not set. The version of Python currently in `PATH` will be used.