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bump ALL gatk4 modules #16620

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bump ALL gatk4 modules

bump ALL gatk4 modules #16620

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Job Run time
prettier
28s
editorconfig
14s
nf-test-changes
3m 3s
pre-commit
46s
pytest-changes
4s
pytest (gatk4/createreadcountpanelofnormals, conda)
2m 34s
pytest (gatk4/createreadcountpanelofnormals, docker)
4m 43s
pytest (gatk4/createreadcountpanelofnormals, singularity)
2m 17s
pytest (gatk4/createsomaticpanelofnormals, conda)
2m 15s
pytest (gatk4/createsomaticpanelofnormals, docker)
3m 32s
pytest (gatk4/createsomaticpanelofnormals, singularity)
2m 15s
pytest (gatk4/determinegermlinecontigploidy, docker)
5m 55s
pytest (gatk4/filtervarianttranches, conda)
2m 18s
pytest (gatk4/filtervarianttranches, docker)
3m 32s
pytest (gatk4/filtervarianttranches, singularity)
2m 38s
pytest (gatk4/germlinecnvcaller, docker)
5m 7s
pytest (gatk4/germlinecnvcaller, singularity)
2m 35s
pytest (gatk4/intervallisttobed, conda)
2m 17s
pytest (gatk4/intervallisttobed, docker)
3m 34s
pytest (gatk4/intervallisttobed, singularity)
2m 12s
pytest (gatk4/printsvevidence, conda)
2m 58s
pytest (gatk4/printsvevidence, docker)
4m 14s
pytest (gatk4/printsvevidence, singularity)
2m 58s
pytest (gatk4/sitedepthtobaf, conda)
2m 19s
pytest (gatk4/sitedepthtobaf, docker)
3m 57s
pytest (gatk4/sitedepthtobaf, singularity)
2m 3s
pytest (gatk4/variantrecalibrator, conda)
2m 29s
pytest (gatk4/variantrecalibrator, docker)
4m 15s
pytest (gatk4/variantrecalibrator, singularity)
3m 12s
nf-core-lint-modules (bam_create_som_pon_gatk)
47s
nf-core-lint-modules (bam_tumor_normal_somatic_variant_calling_strelka)
50s
nf-core-lint-modules (gatk4/applyvqsr)
1m 22s
nf-core-lint-modules (gatk4/collectsvevidence)
1m 10s
nf-core-lint-modules (gatk4/collectreadcounts)
1m 12s
nf-core-lint-modules (gatk4/gatherpileupsummaries)
1m 52s
nf-core-lint-modules (gatk4/gatherbqsrreports)
1m 21s
nf-core-lint-modules (gatk4/mergemutectstats)
2m 1s
nf-core-lint-modules (gatk4/svannotate)
1m 10s
nf-core-lint-modules (gatk4/denoisereadcounts)
1m 51s
nf-core-lint-modules (gatk4/estimatelibrarycomplexity)
1m 22s
nf-core-lint-modules (gatk4/variantfiltration)
1m 29s
nf-core-lint-modules (gatk4)
1m 7s
nf-core-lint-modules (gatk4/baserecalibrator)
1m 23s
nf-core-lint-modules (gatk4/variantstotable)
1m 20s
nf-core-lint-modules (gatk4/calculatecontamination)
1m 9s
nf-core-lint-modules (gatk4/samtofastq)
1m 11s
nf-core-lint-modules (gatk4/genotypegvcfs)
1m 26s
nf-core-lint-modules (gatk4/learnreadorientationmodel)
1m 58s
nf-core-lint-modules (gatk4/revertsam)
1m 23s
nf-core-lint-modules (gatk4/mergebamalignment)
1m 14s
nf-core-lint-modules (gatk4/haplotypecaller)
1m 55s
nf-core-lint-modules (gatk4/intervallisttools)
1m 10s
nf-core-lint-modules (gatk4/filterintervals)
1m 22s
nf-core-lint-modules (gatk4/calibratedragstrmodel)
1m 9s
nf-core-lint-modules (gatk4/addorreplacereadgroups)
1m 9s
nf-core-lint-modules (gatk4/svcluster)
1m 44s
nf-core-lint-modules (gatk4/createsequencedictionary)
1m 11s
nf-core-lint-modules (gatk4/leftalignandtrimvariants)
1m 20s
nf-core-lint-modules (gatk4/shiftfasta)
1m 23s
nf-core-lint-modules (gatk4/splitcram)
1m 19s
nf-core-lint-modules (gatk4/applybqsr)
1m 25s
nf-core-lint-modules (gatk4/indexfeaturefile)
1m 27s
nf-core-lint-modules (gatk4/preprocessintervals)
1m 26s
nf-core-lint-modules (gatk4/markduplicates)
1m 27s
nf-core-lint-modules (gatk4/annotateintervals)
1m 13s
nf-core-lint-modules (gatk4/printreads)
1m 27s
nf-core-lint-modules (gatk4/mutect2)
1m 10s
nf-core-lint-modules (gatk4/selectvariants)
1m 10s
nf-core-lint-modules (gatk4/getpileupsummaries)
1m 12s
nf-core-lint-modules (gatk4/bedtointervallist)
1m 17s
nf-core-lint-modules (gatk4/filtermutectcalls)
1m 10s
nf-core-lint-modules (fastqe)
1m 12s
nf-core-lint-modules (gatk4/fastqtosam)
1m 21s
nf-core-lint-modules (gatk4/splitintervals)
1m 37s
nf-core-lint-modules (gatk4/combinegvcfs)
1m 24s
nf-core-lint-modules (gatk4/composestrtablefile)
1m 42s
nf-core-lint-modules (gatk4/genomicsdbimport)
1m 23s
nf-core-lint-modules (gatk4/splitncigarreads)
1m 26s
nf-core-lint-modules (gatk4/mergevcfs)
2m 3s
nf-core-lint-modules (gatk4/condensedepthevidence)
2m 4s
nf-core-lint-modules (gatk4/reblockgvcf)
1m 23s
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, conda)
15m 41s
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, docker_self_hosted)
6m 18s
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, singularity)
51s
nf-test (modules/nf-core/gatk4/applyvqsr, conda)
5m 32s
nf-test (modules/nf-core/gatk4/applyvqsr, docker_self_hosted)
1m 48s
nf-test (modules/nf-core/gatk4/applyvqsr, singularity)
1m 46s
nf-test (modules/nf-core/gatk4/collectsvevidence, conda)
6m 9s
nf-test (modules/nf-core/gatk4/collectsvevidence, docker_self_hosted)
2m 37s
nf-test (modules/nf-core/gatk4/collectsvevidence, singularity)
1m 54s
nf-test (modules/nf-core/gatk4/collectreadcounts, conda)
4m 51s
nf-test (modules/nf-core/gatk4/collectreadcounts, docker_self_hosted)
1m 45s
nf-test (modules/nf-core/gatk4/collectreadcounts, singularity)
1m 15s
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, conda)
3m 59s
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, docker_self_hosted)
1m 19s
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, singularity)
1m 4s
nf-test (modules/nf-core/gatk4/gatherbqsrreports, conda)
4m 34s
nf-test (modules/nf-core/gatk4/gatherbqsrreports, docker_self_hosted)
56s
nf-test (modules/nf-core/gatk4/gatherbqsrreports, singularity)
1m 15s
nf-test (modules/nf-core/gatk4/mergemutectstats, conda)
5m 5s
nf-test (modules/nf-core/gatk4/mergemutectstats, docker_self_hosted)
1m 18s
nf-test (modules/nf-core/gatk4/mergemutectstats, singularity)
1m 3s
nf-test (modules/nf-core/gatk4/svannotate, conda)
6m 14s
nf-test (modules/nf-core/gatk4/svannotate, docker_self_hosted)
2m 18s
nf-test (modules/nf-core/gatk4/svannotate, singularity)
1m 48s
nf-test (modules/nf-core/gatk4/denoisereadcounts, conda)
3m 59s
nf-test (modules/nf-core/gatk4/denoisereadcounts, docker_self_hosted)
1m 36s
nf-test (modules/nf-core/gatk4/denoisereadcounts, singularity)
51s
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, conda)
4m 58s
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, docker_self_hosted)
3m 5s
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, singularity)
1m 18s
nf-test (modules/nf-core/gatk4/variantfiltration, conda)
5m 4s
nf-test (modules/nf-core/gatk4/variantfiltration, docker_self_hosted)
1m 25s
nf-test (modules/nf-core/gatk4/variantfiltration, singularity)
1m 7s
nf-test (modules/nf-core/gatk4, conda)
33m 8s
nf-test (modules/nf-core/gatk4, docker_self_hosted)
1h 18m 54s
nf-test (modules/nf-core/gatk4, singularity)
36m 7s
nf-test (modules/nf-core/gatk4/baserecalibrator, conda)
4m 33s
nf-test (modules/nf-core/gatk4/baserecalibrator, docker_self_hosted)
4m 25s
nf-test (modules/nf-core/gatk4/baserecalibrator, singularity)
2m 16s
nf-test (modules/nf-core/gatk4/variantstotable, conda)
4m 46s
nf-test (modules/nf-core/gatk4/variantstotable, docker_self_hosted)
2m 36s
nf-test (modules/nf-core/gatk4/variantstotable, singularity)
1m 14s
nf-test (modules/nf-core/gatk4/calculatecontamination, conda)
5m 18s
nf-test (modules/nf-core/gatk4/calculatecontamination, docker_self_hosted)
2m 2s
nf-test (modules/nf-core/gatk4/calculatecontamination, singularity)
1m 28s
nf-test (modules/nf-core/gatk4/samtofastq, conda)
4m 58s
nf-test (modules/nf-core/gatk4/samtofastq, docker_self_hosted)
1s
nf-test (modules/nf-core/gatk4/samtofastq, singularity)
1m 18s
nf-test (modules/nf-core/gatk4/genotypegvcfs, conda)
7m 56s
nf-test (modules/nf-core/gatk4/genotypegvcfs, docker_self_hosted)
3m 20s
nf-test (modules/nf-core/gatk4/genotypegvcfs, singularity)
2m 26s
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, conda)
3m 33s
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, docker_self_hosted)
2m 20s
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, singularity)
48s
nf-test (modules/nf-core/gatk4/revertsam, conda)
4m 35s
nf-test (modules/nf-core/gatk4/revertsam, docker_self_hosted)
1m 16s
nf-test (modules/nf-core/gatk4/revertsam, singularity)
1m 11s
nf-test (modules/nf-core/gatk4/mergebamalignment, conda)
4m 28s
nf-test (modules/nf-core/gatk4/mergebamalignment, docker_self_hosted)
1m 15s
nf-test (modules/nf-core/gatk4/mergebamalignment, singularity)
1m 4s
nf-test (modules/nf-core/gatk4/haplotypecaller, conda)
5m 40s
nf-test (modules/nf-core/gatk4/haplotypecaller, docker_self_hosted)
3m 40s
nf-test (modules/nf-core/gatk4/haplotypecaller, singularity)
1m 32s
nf-test (modules/nf-core/gatk4/intervallisttools, conda)
4m 59s
nf-test (modules/nf-core/gatk4/intervallisttools, docker_self_hosted)
2m 33s
nf-test (modules/nf-core/gatk4/intervallisttools, singularity)
1m 0s
nf-test (modules/nf-core/gatk4/filterintervals, conda)
3m 20s
nf-test (modules/nf-core/gatk4/filterintervals, docker_self_hosted)
57s
nf-test (modules/nf-core/gatk4/filterintervals, singularity)
59s
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, conda)
5m 54s
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, docker_self_hosted)
4m 7s
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, singularity)
1m 35s
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, conda)
4m 34s
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, docker_self_hosted)
3m 44s
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, singularity)
1m 25s
nf-test (modules/nf-core/gatk4/svcluster, conda)
3m 58s
nf-test (modules/nf-core/gatk4/svcluster, docker_self_hosted)
1m 21s
nf-test (modules/nf-core/gatk4/svcluster, singularity)
1m 9s
nf-test (modules/nf-core/gatk4/createsequencedictionary, conda)
4m 17s
nf-test (modules/nf-core/gatk4/createsequencedictionary, docker_self_hosted)
2m 19s
nf-test (modules/nf-core/gatk4/createsequencedictionary, singularity)
1m 15s
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, conda)
5m 2s
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, docker_self_hosted)
2m 28s
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, singularity)
1m 24s
nf-test (modules/nf-core/gatk4/shiftfasta, conda)
2m 8s
nf-test (modules/nf-core/gatk4/shiftfasta, docker_self_hosted)
56s
nf-test (modules/nf-core/gatk4/shiftfasta, singularity)
57s
nf-test (modules/nf-core/gatk4/splitcram, conda)
4m 20s
nf-test (modules/nf-core/gatk4/splitcram, docker_self_hosted)
2m 52s
nf-test (modules/nf-core/gatk4/splitcram, singularity)
1m 15s
nf-test (modules/nf-core/gatk4/applybqsr, conda)
7m 2s
nf-test (modules/nf-core/gatk4/applybqsr, docker_self_hosted)
3m 31s
nf-test (modules/nf-core/gatk4/applybqsr, singularity)
2m 31s
nf-test (modules/nf-core/gatk4/indexfeaturefile, conda)
5m 38s
nf-test (modules/nf-core/gatk4/indexfeaturefile, docker_self_hosted)
2m 12s
nf-test (modules/nf-core/gatk4/indexfeaturefile, singularity)
1m 35s
nf-test (modules/nf-core/gatk4/preprocessintervals, conda)
4m 24s
nf-test (modules/nf-core/gatk4/preprocessintervals, docker_self_hosted)
47s
nf-test (modules/nf-core/gatk4/preprocessintervals, singularity)
49s
nf-test (modules/nf-core/gatk4/markduplicates, conda)
7m 17s
nf-test (modules/nf-core/gatk4/markduplicates, docker_self_hosted)
3m 47s
nf-test (modules/nf-core/gatk4/markduplicates, singularity)
3m 53s
nf-test (modules/nf-core/gatk4/annotateintervals, conda)
7m 14s
nf-test (modules/nf-core/gatk4/annotateintervals, docker_self_hosted)
4m 20s
nf-test (modules/nf-core/gatk4/annotateintervals, singularity)
2m 36s
nf-test (modules/nf-core/gatk4/printreads, conda)
4m 25s
nf-test (modules/nf-core/gatk4/printreads, docker_self_hosted)
2m 39s
nf-test (modules/nf-core/gatk4/printreads, singularity)
1m 14s
nf-test (modules/nf-core/gatk4/mutect2, conda)
39m 16s
nf-test (modules/nf-core/gatk4/mutect2, docker_self_hosted)
4m 57s
nf-test (modules/nf-core/gatk4/mutect2, singularity)
2m 45s
nf-test (modules/nf-core/gatk4/selectvariants, conda)
4m 39s
nf-test (modules/nf-core/gatk4/selectvariants, docker_self_hosted)
2m 36s
nf-test (modules/nf-core/gatk4/selectvariants, singularity)
1m 0s
nf-test (modules/nf-core/gatk4/getpileupsummaries, conda)
7m 39s
nf-test (modules/nf-core/gatk4/getpileupsummaries, docker_self_hosted)
3m 18s
nf-test (modules/nf-core/gatk4/getpileupsummaries, singularity)
1m 42s
nf-test (modules/nf-core/gatk4/bedtointervallist, conda)
3m 16s
nf-test (modules/nf-core/gatk4/bedtointervallist, docker_self_hosted)
58s
nf-test (modules/nf-core/gatk4/bedtointervallist, singularity)
52s
nf-test (modules/nf-core/gatk4/filtermutectcalls, conda)
5m 30s
nf-test (modules/nf-core/gatk4/filtermutectcalls, docker_self_hosted)
3m 23s
nf-test (modules/nf-core/gatk4/filtermutectcalls, singularity)
1m 51s
nf-test (modules/nf-core/fastqe, conda)
4m 25s
nf-test (modules/nf-core/fastqe, docker_self_hosted)
2m 1s
nf-test (modules/nf-core/fastqe, singularity)
2m 35s
nf-test (modules/nf-core/gatk4/fastqtosam, conda)
5m 5s
nf-test (modules/nf-core/gatk4/fastqtosam, docker_self_hosted)
1m 36s
nf-test (modules/nf-core/gatk4/fastqtosam, singularity)
1m 17s
nf-test (modules/nf-core/gatk4/splitintervals, conda)
5m 9s
nf-test (modules/nf-core/gatk4/splitintervals, docker_self_hosted)
2m 50s
nf-test (modules/nf-core/gatk4/splitintervals, singularity)
1m 25s
nf-test (modules/nf-core/gatk4/combinegvcfs, conda)
4m 2s
nf-test (modules/nf-core/gatk4/combinegvcfs, docker_self_hosted)
2m 22s
nf-test (modules/nf-core/gatk4/combinegvcfs, singularity)
1m 2s
nf-test (modules/nf-core/gatk4/composestrtablefile, conda)
3m 29s
nf-test (modules/nf-core/gatk4/composestrtablefile, docker_self_hosted)
2m 32s
nf-test (modules/nf-core/gatk4/composestrtablefile, singularity)
1m 12s
nf-test (modules/nf-core/gatk4/genomicsdbimport, conda)
8m 57s
nf-test (modules/nf-core/gatk4/genomicsdbimport, docker_self_hosted)
3m 40s
nf-test (modules/nf-core/gatk4/genomicsdbimport, singularity)
1m 59s
nf-test (modules/nf-core/gatk4/splitncigarreads, conda)
4m 59s
nf-test (modules/nf-core/gatk4/splitncigarreads, docker_self_hosted)
3m 19s
nf-test (modules/nf-core/gatk4/splitncigarreads, singularity)
1m 15s
nf-test (modules/nf-core/gatk4/mergevcfs, conda)
4m 48s
nf-test (modules/nf-core/gatk4/mergevcfs, docker_self_hosted)
1m 51s
nf-test (modules/nf-core/gatk4/mergevcfs, singularity)
1m 30s
nf-test (modules/nf-core/gatk4/condensedepthevidence, conda)
4m 35s
nf-test (modules/nf-core/gatk4/condensedepthevidence, docker_self_hosted)
1m 14s
nf-test (modules/nf-core/gatk4/condensedepthevidence, singularity)
1m 16s
nf-test (subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka, conda)
4m 8s
nf-test (subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka, docker_self_hosted)
1s
nf-test (subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka, singularity)
2m 22s
nf-test (modules/nf-core/gatk4/reblockgvcf, conda)
4m 53s
nf-test (modules/nf-core/gatk4/reblockgvcf, docker_self_hosted)
1m 45s
nf-test (modules/nf-core/gatk4/reblockgvcf, singularity)
1m 32s
confirm-pass
1s
13h 21m 25s