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bump ALL gatk4 modules #17358

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bump ALL gatk4 modules

bump ALL gatk4 modules #17358

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