bump gatk4 modules #6505

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

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bump gatk4 modules #6505

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bump gatk4 modules #6505

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