bump ALL gatk4 modules #16891

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Job	Run time
editorconfig	11s
pre-commit	40s
nf-test-changes	5m 25s
prettier	32s
pytest-changes	6s
pytest	0s
nf-core-lint-modules (bam_create_som_pon_gatk)	47s
nf-core-lint-modules (bam_tumor_normal_somatic_variant_calling_strelka)	42s
nf-core-lint-modules (gatk4/haplotypecaller)	1m 26s
nf-core-lint-modules (gatk4/composestrtablefile)	1m 30s
nf-core-lint-modules (gatk4/denoisereadcounts)	1m 27s
nf-core-lint-modules (gatk4/gatherbqsrreports)	1m 24s
nf-core-lint-modules (gatk4/estimatelibrarycomplexity)	1m 30s
nf-core-lint-modules (gatk4/bedtointervallist)	1m 24s
nf-core-lint-modules (gatk4/variantrecalibrator)	1m 30s
nf-core-lint-modules (gatk4/mergevcfs)	1m 49s
nf-core-lint-modules (gatk4/splitintervals)	1m 20s
nf-core-lint-modules (gatk4/mergebamalignment)	1m 25s
nf-core-lint-modules (gatk4/svannotate)	1m 22s
nf-core-lint-modules (gatk4/splitcram)	1m 23s
nf-core-lint-modules (gatk4/splitncigarreads)	1m 28s
nf-core-lint-modules (gatk4spark/baserecalibrator)	1m 22s
nf-core-lint-modules (gatk4/filtervarianttranches)	1m 30s
nf-core-lint-modules (gatk4/preprocessintervals)	1m 51s
nf-core-lint-modules (gatk4/calibratedragstrmodel)	1m 22s
nf-core-lint-modules (gatk4/genotypegvcfs)	1m 52s
nf-core-lint-modules (gatk4/germlinecnvcaller)	1m 27s
nf-core-lint-modules (gatk4/applybqsr)	1m 32s
nf-core-lint-modules (gatk4/genomicsdbimport)	1m 52s
nf-core-lint-modules (gatk4/shiftfasta)	1m 48s
nf-core-lint-modules (gatk4/mergemutectstats)	1m 27s
nf-core-lint-modules (gatk4/svcluster)	1m 21s
nf-core-lint-modules (gatk4/combinegvcfs)	1m 49s
nf-core-lint-modules (gatk4/gatherpileupsummaries)	1m 23s
nf-core-lint-modules (gatk4/variantfiltration)	1m 30s
nf-core-lint-modules (gatk4/annotateintervals)	1m 29s
nf-core-lint-modules (gatk4/filtermutectcalls)	1m 28s
nf-core-lint-modules (gatk4/createsomaticpanelofnormals)	1m 28s
nf-core-lint-modules (gatk4/calculatecontamination)	1m 27s
nf-core-lint-modules (gatk4/fastqtosam)	1m 52s
nf-core-lint-modules (gatk4/intervallisttobed)	1m 23s
nf-core-lint-modules (gatk4/collectreadcounts)	1m 32s
nf-core-lint-modules (gatk4/leftalignandtrimvariants)	1m 24s
nf-core-lint-modules (gatk4/getpileupsummaries)	1m 28s
nf-core-lint-modules (gatk4/baserecalibrator)	1m 33s
nf-core-lint-modules (gatk4/printsvevidence)	1m 28s
nf-core-lint-modules (gatk4/determinegermlinecontigploidy)	1m 23s
nf-core-lint-modules (gatk4/printreads)	1m 22s
nf-core-lint-modules (gatk4/markduplicates)	1m 26s
nf-core-lint-modules (gatk4)	1m 19s
nf-core-lint-modules (gatk4/mutect2)	1m 35s
nf-core-lint-modules (gatk4/intervallisttools)	1m 23s
nf-core-lint-modules (gatk4/postprocessgermlinecnvcalls)	1m 31s
nf-core-lint-modules (gatk4/revertsam)	1m 21s
nf-core-lint-modules (gatk4/condensedepthevidence)	1m 23s
nf-core-lint-modules (gatk4/cnnscorevariants)	1m 29s
nf-core-lint-modules (gatk4/learnreadorientationmodel)	1m 27s
nf-core-lint-modules (gatk4/sitedepthtobaf)	1m 50s
nf-core-lint-modules (gatk4/selectvariants)	1m 28s
nf-core-lint-modules (gatk4spark/markduplicates)	1m 26s
nf-core-lint-modules (gatk4/collectsvevidence)	1m 30s
nf-core-lint-modules (gatk4/applyvqsr)	1m 34s
nf-core-lint-modules (gatk4spark/applybqsr)	1m 28s
nf-core-lint-modules (gatk4/createsequencedictionary)	1m 30s
nf-core-lint-modules (gatk4/samtofastq)	1m 24s
nf-test (modules/nf-core/gatk4/haplotypecaller, conda)	6m 53s
nf-test (modules/nf-core/gatk4/haplotypecaller, docker_self_hosted)	2m 36s
nf-test (modules/nf-core/gatk4/haplotypecaller, singularity)	10m 56s
nf-test (modules/nf-core/gatk4/composestrtablefile, conda)	4m 7s
nf-test (modules/nf-core/gatk4/composestrtablefile, docker_self_hosted)	2m 12s
nf-test (modules/nf-core/gatk4/composestrtablefile, singularity)	10m 35s
nf-core-lint-modules (gatk4/reblockgvcf)	1m 20s
nf-test (modules/nf-core/gatk4/denoisereadcounts, conda)	5m 4s
nf-test (modules/nf-core/gatk4/denoisereadcounts, docker_self_hosted)	1m 35s
nf-core-lint-modules (gatk4/indexfeaturefile)	1m 31s
nf-test (modules/nf-core/gatk4/denoisereadcounts, singularity)	9m 7s
nf-core-lint-modules (gatk4/filterintervals)	1m 29s
nf-test (modules/nf-core/gatk4/gatherbqsrreports, conda)	5m 8s
nf-core-lint-modules (gatk4/variantstotable)	1m 25s
nf-test (modules/nf-core/gatk4/gatherbqsrreports, docker_self_hosted)	1m 32s
nf-core-lint-modules (gatk4/addorreplacereadgroups)	1m 22s
nf-test (modules/nf-core/gatk4/gatherbqsrreports, singularity)	10m 47s
nf-core-lint-modules (gatk4/createreadcountpanelofnormals)	1m 30s
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, conda)	5m 22s
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, docker_self_hosted)	3m 12s
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, singularity)	11m 32s
nf-test (modules/nf-core/gatk4/bedtointervallist, conda)	3m 48s
nf-test (modules/nf-core/gatk4/bedtointervallist, docker_self_hosted)	1m 4s
nf-test (modules/nf-core/gatk4/bedtointervallist, singularity)	9m 3s
nf-test (modules/nf-core/gatk4/variantrecalibrator, conda)	5m 27s
nf-test (modules/nf-core/gatk4/variantrecalibrator, docker_self_hosted)	2m 8s
nf-test (modules/nf-core/gatk4/variantrecalibrator, singularity)	10m 13s
nf-test (modules/nf-core/gatk4/mergevcfs, conda)	5m 27s
nf-test (modules/nf-core/gatk4/mergevcfs, docker_self_hosted)	3m 18s
nf-test (modules/nf-core/gatk4/mergevcfs, singularity)	9m 44s
nf-test (modules/nf-core/gatk4/splitintervals, conda)	5m 31s
nf-test (modules/nf-core/gatk4/splitintervals, docker_self_hosted)	1m 49s
nf-test (modules/nf-core/gatk4/splitintervals, singularity)	10m 55s
nf-test (modules/nf-core/gatk4/mergebamalignment, conda)	4m 14s
nf-test (modules/nf-core/gatk4/mergebamalignment, docker_self_hosted)	2m 49s
nf-test (modules/nf-core/gatk4/mergebamalignment, singularity)	8m 49s
nf-test (modules/nf-core/gatk4/svannotate, conda)	6m 5s
nf-test (modules/nf-core/gatk4/svannotate, docker_self_hosted)	2m 36s
nf-test (modules/nf-core/gatk4/svannotate, singularity)	11m 21s
nf-test (modules/nf-core/gatk4/splitcram, conda)	5m 5s
nf-test (modules/nf-core/gatk4/splitcram, docker_self_hosted)	2m 59s
nf-test (modules/nf-core/gatk4/splitcram, singularity)	1m 21s
nf-test (modules/nf-core/gatk4/splitncigarreads, conda)	4m 53s
nf-test (modules/nf-core/gatk4/splitncigarreads, docker_self_hosted)	2m 56s
nf-test (modules/nf-core/gatk4/splitncigarreads, singularity)	10m 52s
nf-test (modules/nf-core/gatk4spark/baserecalibrator, conda)	7m 43s
nf-test (modules/nf-core/gatk4spark/baserecalibrator, docker_self_hosted)	3m 47s
nf-test (modules/nf-core/gatk4spark/baserecalibrator, singularity)	12m 50s
nf-test (modules/nf-core/gatk4/filtervarianttranches, conda)	4m 58s
nf-test (modules/nf-core/gatk4/filtervarianttranches, docker_self_hosted)	1m 22s
nf-test (modules/nf-core/gatk4/filtervarianttranches, singularity)	10m 29s
nf-test (modules/nf-core/gatk4/preprocessintervals, conda)	4m 39s
nf-test (modules/nf-core/gatk4/preprocessintervals, docker_self_hosted)	1m 0s
nf-test (modules/nf-core/gatk4/preprocessintervals, singularity)	7m 9s
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, conda)	5m 53s
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, docker_self_hosted)	2m 26s
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, singularity)	11m 15s
nf-test (modules/nf-core/gatk4/genotypegvcfs, conda)	8m 29s
nf-test (modules/nf-core/gatk4/genotypegvcfs, docker_self_hosted)	4m 54s
nf-test (modules/nf-core/gatk4/genotypegvcfs, singularity)	12m 18s
nf-test (modules/nf-core/gatk4/germlinecnvcaller, conda)	2m 59s
nf-test (modules/nf-core/gatk4/germlinecnvcaller, docker_self_hosted)	9m 20s
nf-test (modules/nf-core/gatk4/germlinecnvcaller, singularity)	23m 54s
nf-test (modules/nf-core/gatk4/applybqsr, conda)	6m 51s
nf-test (modules/nf-core/gatk4/applybqsr, docker_self_hosted)	3m 43s
nf-test (modules/nf-core/gatk4/applybqsr, singularity)	2m 47s
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, conda)	16m 21s
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, docker_self_hosted)	12m 40s
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, singularity)	19m 33s
nf-test (modules/nf-core/gatk4/genomicsdbimport, conda)	6m 16s
nf-test (modules/nf-core/gatk4/genomicsdbimport, docker_self_hosted)	2m 29s
nf-test (modules/nf-core/gatk4/genomicsdbimport, singularity)	11m 33s
nf-test (modules/nf-core/gatk4/shiftfasta, conda)	4m 22s
nf-test (modules/nf-core/gatk4/shiftfasta, docker_self_hosted)	2m 33s
nf-test (modules/nf-core/gatk4/shiftfasta, singularity)	1m 6s
nf-test (modules/nf-core/gatk4/mergemutectstats, conda)	5m 23s
nf-test (modules/nf-core/gatk4/mergemutectstats, docker_self_hosted)	2m 20s
nf-test (modules/nf-core/gatk4/mergemutectstats, singularity)	10m 42s
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)	2m 10s
nf-test (subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka, singularity)	2m 47s
nf-test (modules/nf-core/gatk4/svcluster, conda)	4m 55s
nf-test (modules/nf-core/gatk4/svcluster, docker_self_hosted)	2m 22s
nf-test (modules/nf-core/gatk4/svcluster, singularity)	10m 58s
nf-test (modules/nf-core/gatk4/combinegvcfs, conda)	4m 55s
nf-test (modules/nf-core/gatk4/combinegvcfs, docker_self_hosted)	2m 32s
nf-test (modules/nf-core/gatk4/combinegvcfs, singularity)	11m 37s
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, conda)	4m 25s
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, docker_self_hosted)	2m 55s
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, singularity)	11m 1s
nf-test (modules/nf-core/gatk4/variantfiltration, conda)	4m 27s
nf-test (modules/nf-core/gatk4/variantfiltration, docker_self_hosted)	1m 40s
nf-test (modules/nf-core/gatk4/variantfiltration, singularity)	7m 29s
nf-test (modules/nf-core/gatk4/annotateintervals, conda)	7m 11s
nf-test (modules/nf-core/gatk4/annotateintervals, docker_self_hosted)	2m 49s
nf-test (modules/nf-core/gatk4/annotateintervals, singularity)	3m 10s
nf-test (modules/nf-core/gatk4/filtermutectcalls, conda)	6m 6s
nf-test (modules/nf-core/gatk4/filtermutectcalls, docker_self_hosted)	3m 42s
nf-test (modules/nf-core/gatk4/filtermutectcalls, singularity)	10m 23s
nf-test (modules/nf-core/gatk4/createsomaticpanelofnormals, conda)	4m 41s
nf-test (modules/nf-core/gatk4/createsomaticpanelofnormals, docker_self_hosted)	2m 36s
nf-test (modules/nf-core/gatk4/createsomaticpanelofnormals, singularity)	1m 28s
nf-test (modules/nf-core/gatk4/calculatecontamination, conda)	5m 48s
nf-test (modules/nf-core/gatk4/calculatecontamination, docker_self_hosted)	3m 11s
nf-test (modules/nf-core/gatk4/calculatecontamination, singularity)	2m 11s
nf-test (modules/nf-core/gatk4/fastqtosam, conda)	5m 41s
nf-test (modules/nf-core/gatk4/fastqtosam, docker_self_hosted)	1m 46s
nf-test (modules/nf-core/gatk4/fastqtosam, singularity)	10m 48s
nf-test (modules/nf-core/gatk4/intervallisttobed, conda)	5m 1s
nf-test (modules/nf-core/gatk4/intervallisttobed, docker_self_hosted)	1m 14s
nf-test (modules/nf-core/gatk4/intervallisttobed, singularity)	11m 26s
nf-test (modules/nf-core/gatk4/collectreadcounts, conda)	5m 20s
nf-test (modules/nf-core/gatk4/collectreadcounts, docker_self_hosted)	2m 0s
nf-test (modules/nf-core/gatk4/collectreadcounts, singularity)	1m 52s
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, conda)	5m 32s
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, docker_self_hosted)	2m 29s
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, singularity)	9m 24s
nf-test (modules/nf-core/gatk4/getpileupsummaries, conda)	5m 49s
nf-test (modules/nf-core/gatk4/getpileupsummaries, docker_self_hosted)	3m 22s
nf-test (modules/nf-core/gatk4/getpileupsummaries, singularity)	2m 31s
nf-test (modules/nf-core/gatk4/baserecalibrator, conda)	7m 1s
nf-test (modules/nf-core/gatk4/baserecalibrator, docker_self_hosted)	2m 41s
nf-test (modules/nf-core/gatk4/baserecalibrator, singularity)	11m 56s
nf-test (modules/nf-core/gatk4/printsvevidence, conda)	5m 51s
nf-test (modules/nf-core/gatk4/printsvevidence, docker_self_hosted)	3m 59s
nf-test (modules/nf-core/gatk4/printsvevidence, singularity)	10m 48s
nf-test (modules/nf-core/gatk4/determinegermlinecontigploidy, docker_self_hosted)	7m 31s
nf-test (modules/nf-core/gatk4/determinegermlinecontigploidy, singularity)	23m 40s
nf-test (modules/nf-core/gatk4/printreads, conda)	5m 22s
nf-test (modules/nf-core/gatk4/printreads, docker_self_hosted)	1m 23s
nf-test (modules/nf-core/gatk4/printreads, singularity)	8m 48s
nf-test (modules/nf-core/gatk4/markduplicates, conda)	7m 9s
nf-test (modules/nf-core/gatk4/markduplicates, docker_self_hosted)	3m 37s
nf-test (modules/nf-core/gatk4/markduplicates, singularity)	12m 21s
nf-test (modules/nf-core/gatk4, conda)	43m 8s
nf-test (modules/nf-core/gatk4, docker_self_hosted)	54m 27s
nf-test (modules/nf-core/gatk4, singularity)	50m 40s
nf-test (modules/nf-core/gatk4/mutect2, conda)	39m 2s
nf-test (modules/nf-core/gatk4/mutect2, docker_self_hosted)	36m 10s
nf-test (modules/nf-core/gatk4/mutect2, singularity)	34m 41s
nf-test (modules/nf-core/gatk4/intervallisttools, conda)	4m 52s
nf-test (modules/nf-core/gatk4/intervallisttools, docker_self_hosted)	1m 36s
nf-test (modules/nf-core/gatk4/intervallisttools, singularity)	1m 40s
nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, conda)	3m 40s
nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, docker_self_hosted)	15m 31s
nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, singularity)	15m 29s
nf-test (modules/nf-core/gatk4/revertsam, conda)	5m 35s
nf-test (modules/nf-core/gatk4/revertsam, docker_self_hosted)	1m 17s
nf-test (modules/nf-core/gatk4/revertsam, singularity)	9m 10s
nf-test (modules/nf-core/gatk4/condensedepthevidence, conda)	4m 7s
nf-test (modules/nf-core/gatk4/condensedepthevidence, docker_self_hosted)	1m 23s
nf-test (modules/nf-core/gatk4/condensedepthevidence, singularity)	10m 10s
nf-test (modules/nf-core/gatk4/cnnscorevariants, docker_self_hosted)	6m 0s
nf-test (modules/nf-core/gatk4/cnnscorevariants, singularity)	14m 50s
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, conda)	4m 7s
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, docker_self_hosted)	2m 44s
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, singularity)	1m 22s
nf-test (modules/nf-core/gatk4/sitedepthtobaf, conda)	4m 55s
nf-test (modules/nf-core/gatk4/sitedepthtobaf, docker_self_hosted)	3m 11s
nf-test (modules/nf-core/gatk4/sitedepthtobaf, singularity)	11m 19s
nf-test (modules/nf-core/gatk4/selectvariants, conda)	4m 40s
nf-test (modules/nf-core/gatk4/selectvariants, docker_self_hosted)	2m 32s
nf-test (modules/nf-core/gatk4/selectvariants, singularity)	1m 35s
nf-test (modules/nf-core/gatk4spark/markduplicates, conda)	7m 7s
nf-test (modules/nf-core/gatk4spark/markduplicates, docker_self_hosted)	3m 24s
nf-test (modules/nf-core/gatk4spark/markduplicates, singularity)	12m 37s
nf-test (modules/nf-core/gatk4/collectsvevidence, conda)	6m 55s
nf-test (modules/nf-core/gatk4/collectsvevidence, docker_self_hosted)	2m 39s
nf-test (modules/nf-core/gatk4/collectsvevidence, singularity)	2m 37s
nf-test (modules/nf-core/gatk4/applyvqsr, conda)	5m 42s
nf-test (modules/nf-core/gatk4/applyvqsr, docker_self_hosted)	2m 56s
nf-test (modules/nf-core/gatk4/applyvqsr, singularity)	2m 6s
nf-test (modules/nf-core/gatk4spark/applybqsr, conda)	6m 28s
nf-test (modules/nf-core/gatk4spark/applybqsr, docker_self_hosted)	2m 55s
nf-test (modules/nf-core/gatk4spark/applybqsr, singularity)	11m 20s
nf-test (modules/nf-core/gatk4/createsequencedictionary, conda)	4m 7s
nf-test (modules/nf-core/gatk4/createsequencedictionary, docker_self_hosted)	2m 32s
nf-test (modules/nf-core/gatk4/createsequencedictionary, singularity)	7m 46s
nf-test (modules/nf-core/gatk4/samtofastq, conda)	5m 40s
nf-test (modules/nf-core/gatk4/samtofastq, docker_self_hosted)	2m 58s
nf-test (modules/nf-core/gatk4/samtofastq, singularity)	10m 15s
nf-test (modules/nf-core/gatk4/reblockgvcf, conda)	5m 35s
nf-test (modules/nf-core/gatk4/reblockgvcf, docker_self_hosted)	2m 50s
nf-test (modules/nf-core/gatk4/reblockgvcf, singularity)	1m 47s
nf-test (modules/nf-core/gatk4/indexfeaturefile, conda)	6m 6s
nf-test (modules/nf-core/gatk4/indexfeaturefile, docker_self_hosted)	3m 44s
nf-test (modules/nf-core/gatk4/indexfeaturefile, singularity)	11m 13s
nf-test (modules/nf-core/gatk4/filterintervals, conda)	3m 49s
nf-test (modules/nf-core/gatk4/filterintervals, docker_self_hosted)	2m 8s
nf-test (modules/nf-core/gatk4/filterintervals, singularity)	10m 43s
nf-test (modules/nf-core/gatk4/variantstotable, conda)	4m 34s
nf-test (modules/nf-core/gatk4/variantstotable, docker_self_hosted)	2m 56s
nf-test (modules/nf-core/gatk4/variantstotable, singularity)	1m 20s
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, conda)	5m 3s
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, docker_self_hosted)	1m 53s
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, singularity)	8m 13s
nf-test (modules/nf-core/gatk4/createreadcountpanelofnormals, conda)	5m 43s
nf-test (modules/nf-core/gatk4/createreadcountpanelofnormals, docker_self_hosted)	2m 20s
nf-test (modules/nf-core/gatk4/createreadcountpanelofnormals, singularity)	12m 42s
confirm-pass	4s
	1d 0h 30m 13s

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bump ALL gatk4 modules #16891

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bump ALL gatk4 modules #16891

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