bump ALL gatk4 modules #17381

Run time

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Job	Run time
nf-test-changes	5m 21s
editorconfig	11s
pre-commit	41s
prettier	30s
pytest-changes	10s
pytest	0s
nf-test-gpu	0s
nf-core-lint-modules (bam_tumor_normal_somatic_variant_calling_strelka)	51s
nf-core-lint-modules (bam_create_som_pon_gatk)	51s
nf-core-lint-modules (gatk4/filtervarianttranches)	47s
nf-core-lint-modules (gatk4/condensedepthevidence)	49s
nf-core-lint-modules (gatk4/applyvqsr)	51s
nf-core-lint-modules (gatk4/genomicsdbimport)	56s
nf-core-lint-modules (gatk4/genotypegvcfs)	57s
nf-core-lint-modules (gatk4/combinegvcfs)	52s
nf-core-lint-modules (gatk4/printreads)	47s
nf-core-lint-modules (gatk4/fastqtosam)	46s
nf-core-lint-modules (gatk4/variantstotable)	55s
nf-core-lint-modules (gatk4/estimatelibrarycomplexity)	56s
nf-core-lint-modules (gatk4/createreadcountpanelofnormals)	53s
nf-core-lint-modules (gatk4/mergebamalignment)	55s
nf-core-lint-modules (gatk4/baserecalibrator)	55s
nf-core-lint-modules (gatk4/reblockgvcf)	51s
nf-core-lint-modules (gatk4/germlinecnvcaller)	49s
nf-core-lint-modules (gatk4/leftalignandtrimvariants)	50s
nf-core-lint-modules (gatk4/haplotypecaller)	50s
nf-core-lint-modules (gatk4/getpileupsummaries)	1m 1s
nf-core-lint-modules (gatk4spark/baserecalibrator)	58s
nf-core-lint-modules (gatk4/variantfiltration)	50s
nf-core-lint-modules (gatk4/splitintervals)	56s
nf-core-lint-modules (gatk4/splitcram)	51s
nf-core-lint-modules (gatk4/shiftfasta)	56s
nf-core-lint-modules (gatk4/gatherbqsrreports)	56s
nf-core-lint-modules (gatk4/calibratedragstrmodel)	45s
nf-core-lint-modules (gatk4/selectvariants)	52s
nf-core-lint-modules (gatk4/printsvevidence)	48s
nf-core-lint-modules (gatk4spark/markduplicates)	44s
nf-core-lint-modules (gatk4)	52s
nf-core-lint-modules (gatk4/composestrtablefile)	1m 5s
nf-core-lint-modules (gatk4/learnreadorientationmodel)	49s
nf-core-lint-modules (gatk4/applybqsr)	55s
nf-core-lint-modules (gatk4/addorreplacereadgroups)	54s
nf-core-lint-modules (gatk4/filtermutectcalls)	45s
nf-core-lint-modules (gatk4/collectsvevidence)	49s
nf-core-lint-modules (gatk4/postprocessgermlinecnvcalls)	43s
nf-core-lint-modules (gatk4/createsequencedictionary)	57s
nf-core-lint-modules (gatk4/mergevcfs)	56s
nf-core-lint-modules (gatk4/indexfeaturefile)	43s
nf-core-lint-modules (gatk4/intervallisttools)	53s
nf-core-lint-modules (gatk4/variantrecalibrator)	57s
nf-core-lint-modules (gatk4/cnnscorevariants)	54s
nf-core-lint-modules (gatk4/svcluster)	57s
nf-core-lint-modules (gatk4/denoisereadcounts)	49s
nf-core-lint-modules (gatk4/determinegermlinecontigploidy)	1m 14s
nf-core-lint-modules (gatk4/sitedepthtobaf)	58s
nf-core-lint-modules (gatk4/revertsam)	52s
nf-core-lint-modules (gatk4/intervallisttobed)	53s
nf-core-lint-modules (gatk4spark/applybqsr)	51s
nf-core-lint-modules (gatk4/calculatecontamination)	1m 6s
nf-core-lint-modules (gatk4/filterintervals)	55s
nf-core-lint-modules (gatk4/annotateintervals)	57s
nf-core-lint-modules (gatk4/samtofastq)	48s
nf-core-lint-modules (gatk4/gatherpileupsummaries)	55s
nf-core-lint-modules (gatk4/preprocessintervals)	45s
nf-core-lint-modules (gatk4/collectreadcounts)	54s
nf-core-lint-modules (gatk4/bedtointervallist)	55s
nf-core-lint-modules (gatk4/svannotate)	48s
nf-core-lint-modules (gatk4/createsomaticpanelofnormals)	45s
nf-core-lint-modules (gatk4/mergemutectstats)	53s
nf-core-lint-modules (gatk4/markduplicates)	55s
nf-core-lint-modules (gatk4/splitncigarreads)	44s
nf-core-lint-modules (gatk4/mutect2)	57s
nf-test (modules/nf-core/gatk4/filtervarianttranches, conda)	10m 12s
nf-test (modules/nf-core/gatk4/filtervarianttranches, docker_self_hosted)	6m 56s
nf-test (modules/nf-core/gatk4/filtervarianttranches, singularity)	3m 7s
nf-test (modules/nf-core/gatk4/condensedepthevidence, conda)	9m 41s
nf-test (modules/nf-core/gatk4/condensedepthevidence, docker_self_hosted)	6m 50s
nf-test (modules/nf-core/gatk4/condensedepthevidence, singularity)	2m 41s
nf-test (modules/nf-core/gatk4/applyvqsr, conda)	11m 35s
nf-test (modules/nf-core/gatk4/applyvqsr, docker_self_hosted)	7m 8s
nf-test (modules/nf-core/gatk4/applyvqsr, singularity)	2m 16s
nf-test (modules/nf-core/gatk4/genomicsdbimport, conda)	16m 40s
nf-test (modules/nf-core/gatk4/genomicsdbimport, docker_self_hosted)	7m 33s
nf-test (modules/nf-core/gatk4/genomicsdbimport, singularity)	2m 47s
nf-test (modules/nf-core/gatk4/genotypegvcfs, conda)	22m 8s
nf-test (modules/nf-core/gatk4/genotypegvcfs, docker_self_hosted)	9m 5s
nf-test (modules/nf-core/gatk4/genotypegvcfs, singularity)	4m 42s
nf-test (subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka, conda)	5m 56s
nf-test (subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka, docker_self_hosted)	3m 16s
nf-test (subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_strelka, singularity)	1s
nf-test (modules/nf-core/gatk4/combinegvcfs, conda)	10m 48s
nf-test (modules/nf-core/gatk4/combinegvcfs, docker_self_hosted)	6m 24s
nf-test (modules/nf-core/gatk4/combinegvcfs, singularity)	1m 27s
nf-test (modules/nf-core/gatk4/printreads, conda)	3m 20s
nf-test (modules/nf-core/gatk4/printreads, docker_self_hosted)	3m 43s
nf-test (modules/nf-core/gatk4/printreads, singularity)	2m 48s
nf-test (modules/nf-core/gatk4/fastqtosam, conda)	11m 29s
nf-test (modules/nf-core/gatk4/fastqtosam, docker_self_hosted)	7m 59s
nf-test (modules/nf-core/gatk4/fastqtosam, singularity)	3m 51s
nf-test (modules/nf-core/gatk4/variantstotable, conda)	8m 18s
nf-test (modules/nf-core/gatk4/variantstotable, docker_self_hosted)	6m 43s
nf-test (modules/nf-core/gatk4/variantstotable, singularity)	1m 29s
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, conda)	12m 49s
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, docker_self_hosted)	6m 45s
nf-test (modules/nf-core/gatk4/estimatelibrarycomplexity, singularity)	2m 12s
nf-test (modules/nf-core/gatk4/createreadcountpanelofnormals, conda)	10m 40s
nf-test (modules/nf-core/gatk4/createreadcountpanelofnormals, docker_self_hosted)	5m 45s
nf-test (modules/nf-core/gatk4/createreadcountpanelofnormals, singularity)	3m 46s
nf-test (modules/nf-core/gatk4/mergebamalignment, conda)	8m 51s
nf-test (modules/nf-core/gatk4/mergebamalignment, docker_self_hosted)	6m 7s
nf-test (modules/nf-core/gatk4/mergebamalignment, singularity)	2m 1s
nf-test (modules/nf-core/gatk4/baserecalibrator, conda)	7m 57s
nf-test (modules/nf-core/gatk4/baserecalibrator, docker_self_hosted)	8m 7s
nf-test (modules/nf-core/gatk4/baserecalibrator, singularity)	3m 53s
nf-test (modules/nf-core/gatk4/reblockgvcf, conda)	12m 28s
nf-test (modules/nf-core/gatk4/reblockgvcf, docker_self_hosted)	1m 58s
nf-test (modules/nf-core/gatk4/reblockgvcf, singularity)	3m 2s
nf-test (modules/nf-core/gatk4/germlinecnvcaller, conda)	2m 6s
nf-test (modules/nf-core/gatk4/germlinecnvcaller, docker_self_hosted)	25m 9s
nf-test (modules/nf-core/gatk4/germlinecnvcaller, singularity)	20m 50s
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, conda)	8m 43s
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, docker_self_hosted)	7m 49s
nf-test (modules/nf-core/gatk4/leftalignandtrimvariants, singularity)	2m 8s
nf-test (modules/nf-core/gatk4/haplotypecaller, conda)	15m 9s
nf-test (modules/nf-core/gatk4/haplotypecaller, docker_self_hosted)	8m 26s
nf-test (modules/nf-core/gatk4/haplotypecaller, singularity)	4m 23s
nf-test (modules/nf-core/gatk4/getpileupsummaries, conda)	11m 56s
nf-test (modules/nf-core/gatk4/getpileupsummaries, docker_self_hosted)	8m 1s
nf-test (modules/nf-core/gatk4/getpileupsummaries, singularity)	3m 15s
nf-test (modules/nf-core/gatk4spark/baserecalibrator, conda)	39s
nf-test (modules/nf-core/gatk4spark/baserecalibrator, docker_self_hosted)	3m 20s
nf-test (modules/nf-core/gatk4spark/baserecalibrator, singularity)	5m 50s
nf-test (modules/nf-core/gatk4/variantfiltration, conda)	8m 48s
nf-test (modules/nf-core/gatk4/variantfiltration, docker_self_hosted)	1m 27s
nf-test (modules/nf-core/gatk4/variantfiltration, singularity)	2m 35s
nf-test (modules/nf-core/gatk4/splitintervals, conda)	11m 14s
nf-test (modules/nf-core/gatk4/splitintervals, docker_self_hosted)	6m 25s
nf-test (modules/nf-core/gatk4/splitintervals, singularity)	2m 0s
nf-test (modules/nf-core/gatk4/splitcram, conda)	9m 24s
nf-test (modules/nf-core/gatk4/splitcram, docker_self_hosted)	2m 51s
nf-test (modules/nf-core/gatk4/splitcram, singularity)	2m 1s
nf-test (modules/nf-core/gatk4/shiftfasta, conda)	7m 8s
nf-test (modules/nf-core/gatk4/shiftfasta, docker_self_hosted)	1m 12s
nf-test (modules/nf-core/gatk4/shiftfasta, singularity)	2m 20s
nf-test (modules/nf-core/gatk4/gatherbqsrreports, conda)	11m 33s
nf-test (modules/nf-core/gatk4/gatherbqsrreports, docker_self_hosted)	6m 20s
nf-test (modules/nf-core/gatk4/gatherbqsrreports, singularity)	2m 25s
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, conda)	16m 37s
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, docker_self_hosted)	8m 8s
nf-test (modules/nf-core/gatk4/calibratedragstrmodel, singularity)	5m 51s
nf-test (modules/nf-core/gatk4/selectvariants, conda)	10m 25s
nf-test (modules/nf-core/gatk4/selectvariants, docker_self_hosted)	1m 31s
nf-test (modules/nf-core/gatk4/selectvariants, singularity)	1m 57s
nf-test (modules/nf-core/gatk4/printsvevidence, conda)	9m 22s
nf-test (modules/nf-core/gatk4/printsvevidence, docker_self_hosted)	7m 44s
nf-test (modules/nf-core/gatk4/printsvevidence, singularity)	2m 55s
nf-test (modules/nf-core/gatk4spark/markduplicates, conda)	8m 12s
nf-test (modules/nf-core/gatk4spark/markduplicates, docker_self_hosted)	3m 30s
nf-test (modules/nf-core/gatk4spark/markduplicates, singularity)	5m 12s
nf-test (modules/nf-core/gatk4, conda)	1h 1m 24s
nf-test (modules/nf-core/gatk4, docker_self_hosted)	52m 50s
nf-test (modules/nf-core/gatk4, singularity)	47m 45s
nf-test (modules/nf-core/gatk4/composestrtablefile, conda)	6m 14s
nf-test (modules/nf-core/gatk4/composestrtablefile, docker_self_hosted)	5m 15s
nf-test (modules/nf-core/gatk4/composestrtablefile, singularity)	2m 19s
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, conda)	7m 49s
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, docker_self_hosted)	5m 55s
nf-test (modules/nf-core/gatk4/learnreadorientationmodel, singularity)	2m 29s
nf-test (modules/nf-core/gatk4/applybqsr, conda)	17m 54s
nf-test (modules/nf-core/gatk4/applybqsr, docker_self_hosted)	8m 6s
nf-test (modules/nf-core/gatk4/applybqsr, singularity)	4m 0s
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, conda)	12m 55s
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, docker_self_hosted)	1s
nf-test (modules/nf-core/gatk4/addorreplacereadgroups, singularity)	3m 11s
nf-test (modules/nf-core/gatk4/filtermutectcalls, conda)	16m 8s
nf-test (modules/nf-core/gatk4/filtermutectcalls, docker_self_hosted)	7m 28s
nf-test (modules/nf-core/gatk4/filtermutectcalls, singularity)	4m 59s
nf-test (modules/nf-core/gatk4/collectsvevidence, conda)	16m 8s
nf-test (modules/nf-core/gatk4/collectsvevidence, docker_self_hosted)	7m 34s
nf-test (modules/nf-core/gatk4/collectsvevidence, singularity)	4m 7s
nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, conda)	1m 41s
nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, docker_self_hosted)	3m 35s
nf-test (modules/nf-core/gatk4/postprocessgermlinecnvcalls, singularity)	1s
nf-test (modules/nf-core/gatk4/createsequencedictionary, conda)	11m 25s
nf-test (modules/nf-core/gatk4/createsequencedictionary, docker_self_hosted)	6m 31s
nf-test (modules/nf-core/gatk4/createsequencedictionary, singularity)	2m 30s
nf-test (modules/nf-core/gatk4/mergevcfs, conda)	11m 31s
nf-test (modules/nf-core/gatk4/mergevcfs, docker_self_hosted)	2m 2s
nf-test (modules/nf-core/gatk4/mergevcfs, singularity)	2m 57s
nf-test (modules/nf-core/gatk4/indexfeaturefile, conda)	13m 22s
nf-test (modules/nf-core/gatk4/indexfeaturefile, docker_self_hosted)	6m 58s
nf-test (modules/nf-core/gatk4/indexfeaturefile, singularity)	3m 36s
nf-test (modules/nf-core/gatk4/intervallisttools, conda)	4m 47s
nf-test (modules/nf-core/gatk4/intervallisttools, docker_self_hosted)	6m 28s
nf-test (modules/nf-core/gatk4/intervallisttools, singularity)	2m 42s
nf-test (modules/nf-core/gatk4/variantrecalibrator, conda)	14m 8s
nf-test (modules/nf-core/gatk4/variantrecalibrator, docker_self_hosted)	7m 35s
nf-test (modules/nf-core/gatk4/variantrecalibrator, singularity)	2m 18s
nf-test (modules/nf-core/gatk4/cnnscorevariants, docker_self_hosted)	6m 56s
nf-test (modules/nf-core/gatk4/cnnscorevariants, singularity)	15m 8s
nf-test (modules/nf-core/gatk4/svcluster, conda)	7m 1s
nf-test (modules/nf-core/gatk4/svcluster, docker_self_hosted)	6m 31s
nf-test (modules/nf-core/gatk4/svcluster, singularity)	2m 55s
nf-test (modules/nf-core/gatk4/denoisereadcounts, conda)	8m 43s
nf-test (modules/nf-core/gatk4/denoisereadcounts, docker_self_hosted)	6m 21s
nf-test (modules/nf-core/gatk4/denoisereadcounts, singularity)	3m 53s
nf-test (modules/nf-core/gatk4/determinegermlinecontigploidy, docker_self_hosted)	16m 8s
nf-test (modules/nf-core/gatk4/determinegermlinecontigploidy, singularity)	12m 23s
nf-test (modules/nf-core/gatk4/sitedepthtobaf, conda)	11m 52s
nf-test (modules/nf-core/gatk4/sitedepthtobaf, docker_self_hosted)	7m 57s
nf-test (modules/nf-core/gatk4/sitedepthtobaf, singularity)	3m 16s
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, conda)	22m 6s
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, docker_self_hosted)	18m 1s
nf-test (subworkflows/nf-core/bam_create_som_pon_gatk, singularity)	15m 11s
nf-test (modules/nf-core/gatk4/revertsam, conda)	10m 5s
nf-test (modules/nf-core/gatk4/revertsam, docker_self_hosted)	3m 15s
nf-test (modules/nf-core/gatk4/revertsam, singularity)	1m 38s
nf-test (modules/nf-core/gatk4/intervallisttobed, conda)	9m 17s
nf-test (modules/nf-core/gatk4/intervallisttobed, docker_self_hosted)	6m 31s
nf-test (modules/nf-core/gatk4/intervallisttobed, singularity)	2m 33s
nf-test (modules/nf-core/gatk4spark/applybqsr, conda)	5m 39s
nf-test (modules/nf-core/gatk4spark/applybqsr, docker_self_hosted)	3m 9s
nf-test (modules/nf-core/gatk4spark/applybqsr, singularity)	6m 2s
nf-test (modules/nf-core/gatk4/calculatecontamination, conda)	15m 56s
nf-test (modules/nf-core/gatk4/calculatecontamination, docker_self_hosted)	7m 47s
nf-test (modules/nf-core/gatk4/calculatecontamination, singularity)	3m 27s
nf-test (modules/nf-core/gatk4/filterintervals, conda)	6m 34s
nf-test (modules/nf-core/gatk4/filterintervals, docker_self_hosted)	6m 45s
nf-test (modules/nf-core/gatk4/filterintervals, singularity)	2m 13s
nf-test (modules/nf-core/gatk4/annotateintervals, conda)	22m 1s
nf-test (modules/nf-core/gatk4/annotateintervals, docker_self_hosted)	9m 2s
nf-test (modules/nf-core/gatk4/annotateintervals, singularity)	4m 18s
nf-test (modules/nf-core/gatk4/samtofastq, conda)	11m 26s
nf-test (modules/nf-core/gatk4/samtofastq, docker_self_hosted)	7m 5s
nf-test (modules/nf-core/gatk4/samtofastq, singularity)	2m 49s
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, conda)	9m 38s
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, docker_self_hosted)	6m 24s
nf-test (modules/nf-core/gatk4/gatherpileupsummaries, singularity)	2m 23s
nf-test (modules/nf-core/gatk4/preprocessintervals, conda)	1s
nf-test (modules/nf-core/gatk4/preprocessintervals, docker_self_hosted)	5m 53s
nf-test (modules/nf-core/gatk4/preprocessintervals, singularity)	2m 17s
nf-test (modules/nf-core/gatk4/collectreadcounts, conda)	12m 1s
nf-test (modules/nf-core/gatk4/collectreadcounts, docker_self_hosted)	6m 52s
nf-test (modules/nf-core/gatk4/collectreadcounts, singularity)	3m 3s
nf-test (modules/nf-core/gatk4/bedtointervallist, conda)	8m 59s
nf-test (modules/nf-core/gatk4/bedtointervallist, docker_self_hosted)	6m 18s
nf-test (modules/nf-core/gatk4/bedtointervallist, singularity)	2m 20s
nf-test (modules/nf-core/gatk4/svannotate, conda)	12m 40s
nf-test (modules/nf-core/gatk4/svannotate, docker_self_hosted)	7m 45s
nf-test (modules/nf-core/gatk4/svannotate, singularity)	3m 58s
nf-test (modules/nf-core/gatk4/createsomaticpanelofnormals, conda)	11m 7s
nf-test (modules/nf-core/gatk4/createsomaticpanelofnormals, docker_self_hosted)	6m 38s
nf-test (modules/nf-core/gatk4/createsomaticpanelofnormals, singularity)	2m 40s
nf-test (modules/nf-core/gatk4/mergemutectstats, conda)	3m 56s
nf-test (modules/nf-core/gatk4/mergemutectstats, docker_self_hosted)	5m 49s
nf-test (modules/nf-core/gatk4/mergemutectstats, singularity)	2m 22s
nf-test (modules/nf-core/gatk4/markduplicates, conda)	14m 18s
nf-test (modules/nf-core/gatk4/markduplicates, docker_self_hosted)	4m 8s
nf-test (modules/nf-core/gatk4/markduplicates, singularity)	4m 26s
nf-test (modules/nf-core/gatk4/splitncigarreads, conda)	37s
nf-test (modules/nf-core/gatk4/splitncigarreads, docker_self_hosted)	7m 5s
nf-test (modules/nf-core/gatk4/splitncigarreads, singularity)	3m 4s
nf-test (modules/nf-core/gatk4/mutect2, conda)	49m 42s
nf-test (modules/nf-core/gatk4/mutect2, docker_self_hosted)	46m 27s
nf-test (modules/nf-core/gatk4/mutect2, singularity)	41m 9s
confirm-pass	1s
	1d 3h 32m 32s

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bump ALL gatk4 modules #17381

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bump ALL gatk4 modules #17381

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