gatk4 - convert versions from modules to topics #9738
Description
cf https://github.com/maxulysse/nf-core_modules/tree/even_more_gatk4
Is your feature request related to a problem? Please describe
- gatk4/addorreplacereadgroups - gatk4 modules a* and b* convertion to topics for versions #9729
- gatk4/annotateintervals - gatk4 modules a* and b* convertion to topics for versions #9729
- gatk4/applybqsr - gatk4 modules a* and b* convertion to topics for versions #9729
- gatk4/applyvqsr - gatk4 modules a* and b* convertion to topics for versions #9729
- gatk4/asereadcounter - gatk4 modules a* and b* convertion to topics for versions #9729
- gatk4/baserecalibrator - gatk4 modules a* and b* convertion to topics for versions #9729
- gatk4/bedtointervallist - gatk4/bedtointervallist #9737
- gatk4/calculatecontamination
- gatk4/calibratedragstrmodel
- gatk4/cnnscorevariants
- gatk4/collectreadcounts
- gatk4/collectsvevidence
- gatk4/combinegvcfs
- gatk4/composestrtablefile
- gatk4/concordance
- gatk4/condensedepthevidence
- gatk4/createreadcountpanelofnormals
- gatk4/createsequencedictionary
- gatk4/createsomaticpanelofnormals
- gatk4/denoisereadcounts
- gatk4/determinegermlinecontigploidy
- gatk4/estimatelibrarycomplexity
- gatk4/fastqtosam
- gatk4/filterintervals
- gatk4/filtermutectcalls
- gatk4/filtervarianttranches
- gatk4/gatherbqsrreports
- gatk4/gatherpileupsummaries
- gatk4/genomicsdbimport
- gatk4/genotypegvcfs
- gatk4/germlinecnvcaller
- gatk4/getpileupsummaries
- gatk4/haplotypecaller
- gatk4/indexfeaturefile
- gatk4/intervallisttobed
- gatk4/intervallisttools
- gatk4/learnreadorientationmodel
- gatk4/leftalignandtrimvariants
- gatk4/markduplicates
- gatk4/mergebamalignment
- gatk4/mergemutectstats
- gatk4/mergevcfs
- gatk4/modelsegments
- gatk4/mutect2
- gatk4/postprocessgermlinecnvcalls
- gatk4/preprocessintervals
- gatk4/printreads
- gatk4/printsvevidence
- gatk4/reblockgvcf
- gatk4/revertsam
- gatk4/samtofastq
- gatk4/selectvariants
- gatk4/shiftfasta
- gatk4/sitedepthtobaf
- gatk4/splitcram
- gatk4/splitintervals
- gatk4/splitncigarreads
- gatk4/svannotate
- gatk4/svcluster
- gatk4/unmarkduplicates
- gatk4/variantfiltration
- gatk4/variantrecalibrator
- gatk4/variantstotable
- gatk4spark/applybqsr - gatk4spark #9728
- gatk4spark/baserecalibrator - gatk4spark #9728
- gatk4spark/markduplicates - gatk4spark #9728
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