diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index d2286a7018c..3893bf75737 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -1,1104 +1,14 @@
-*.nf.test* @nf-core/nf-test
-.github/workflows/test.yml @nf-core/nf-test
-tags.yml @nf-core/nf-test
-tests/config @nf-core/nf-test
-modules/nf-core/abacas/** @joseespinosa @drpatelh
-modules/nf-core/abricate/run/** @rpetit3
-modules/nf-core/abricate/summary/** @rpetit3
-modules/nf-core/abritamr/run/** @rpetit3
-modules/nf-core/adapterremovalfixprefix/** @jfy133
-modules/nf-core/adapterremoval/** @maxibor @jfy133
-modules/nf-core/admixture/** @atrigila
-modules/nf-core/affy/justrma/** @pinin4fjords
-modules/nf-core/agat/convertspgff2gtf/** @toniher
-modules/nf-core/agat/convertspgxf2gxf/** @toniher
-modules/nf-core/agat/spstatistics/** @toniher
-modules/nf-core/agat/sqstatbasic/** @toniher
-modules/nf-core/agrvate/** @abhi18av
-modules/nf-core/allelecounter/** @fullama @fbdtemme
-modules/nf-core/ampcombi/** @darcy220606 @louperelo
-modules/nf-core/ampir/** @jasmezz
-modules/nf-core/amplify/predict/** @louperelo
-modules/nf-core/amps/** @jfy133
-modules/nf-core/amrfinderplus/run/** @rpetit3 @louperelo @jfy133
-modules/nf-core/amrfinderplus/update/** @rpetit3
-modules/nf-core/angsd/contamination/** @jbv2
-modules/nf-core/angsd/docounts/** @jfy133
-modules/nf-core/annotsv/annotsv/** @nvnieuwk
-modules/nf-core/annotsv/installannotations/** @nvnieuwk
-modules/nf-core/antismash/antismashlitedownloaddatabases/** @jasmezz
-modules/nf-core/antismash/antismashlite/** @jasmezz
-modules/nf-core/arcashla/extract/** @christopher-mohr
-modules/nf-core/aria2/** @JoseEspinosa
-modules/nf-core/ariba/getref/** @rpetit3
-modules/nf-core/ariba/run/** @rpetit3
-modules/nf-core/arriba/arriba/** @praveenraj2018,@rannick
-modules/nf-core/artic/guppyplex/** @joseespinosa @drpatelh
-modules/nf-core/artic/minion/** @joseespinosa @drpatelh
-modules/nf-core/art/illumina/** @MarieLataretu
-modules/nf-core/ascat/** @aasNGC @lassefolkersen @FriederikeHanssen @maxulysse @SusiJo
-modules/nf-core/ashlar/** @RobJY @jmuhlich
-modules/nf-core/assemblyscan/** @sateeshperi @mjcipriano
-modules/nf-core/ataqv/ataqv/** @i-pletenev
-modules/nf-core/ataqv/mkarv/** @bjlang
-modules/nf-core/atlas/call/** @jfy133
-modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/** @pinin4fjords
-modules/nf-core/atlas/pmd/** @maxibor @merszym
-modules/nf-core/atlas/recal/** @ltcrod
-modules/nf-core/atlas/splitmerge/** @merszym
-modules/nf-core/authentict/deam2cont/** @scarlhoff @StephanePeyregne
-modules/nf-core/backsub/** @kbestak
-modules/nf-core/bacphlip/** @CarsonJM
-modules/nf-core/bakta/baktadbdownload/** @jfy133 @jasmezz
-modules/nf-core/bakta/bakta/** @rpetit3 @oschwengers @jfy133
-modules/nf-core/bamaligncleaner/** @jfy133
-modules/nf-core/bamcmp/** @kmurat1 @sppearce
-modules/nf-core/bamtools/convert/** @sguizard
-modules/nf-core/bamtools/split/** @sguizard @matthdsm
-modules/nf-core/bamtools/stats/** @lescai
-modules/nf-core/bamutil/trimbam/** @jfy133
-modules/nf-core/bandage/image/** @heuermh
-modules/nf-core/barrnap/** @danilodileo
-modules/nf-core/bases2fastq/** @edmundmiller
-modules/nf-core/basicpy/** @FloWuenne
-modules/nf-core/bbmap/align/** @erikrikarddaniel
-modules/nf-core/bbmap/bbduk/** @MGordon09
-modules/nf-core/bbmap/bbnorm/** @danilodileo
-modules/nf-core/bbmap/bbsplit/** @joseespinosa @drpatelh
-modules/nf-core/bbmap/clumpify/** @tamuanand
-modules/nf-core/bbmap/index/** @daniellundin
-modules/nf-core/bbmap/pileup/** @edmundmiller
-modules/nf-core/bbmap/sendsketch/** @phanhung2
-modules/nf-core/bcftools/annotate/** @projectoriented @ramprasadn
-modules/nf-core/bcftools/call/** @abhi18av @LouisLeNezet
-modules/nf-core/bcftools/concat/** @abhi18av @nvnieuwk
-modules/nf-core/bcftools/consensus/** @joseespinosa @drpatelh
-modules/nf-core/bcftools/convert/** @nvnieuwk @ramprasadn @atrigila
-modules/nf-core/bcftools/filter/** @joseespinosa @drpatelh
-modules/nf-core/bcftools/index/** @jfy133
-modules/nf-core/bcftools/isec/** @joseespinosa @drpatelh
-modules/nf-core/bcftools/merge/** @joseespinosa @drpatelh @nvnieuwk @ramprasadn
-modules/nf-core/bcftools/mpileup/** @joseespinosa @drpatelh
-modules/nf-core/bcftools/norm/** @abhi18av @ramprasadn
-modules/nf-core/bcftools/pluginscatter/** @nvnieuwk
-modules/nf-core/bcftools/pluginsplit/** @nvnieuwk
-modules/nf-core/bcftools/query/** @abhi18av @drpatelh
-modules/nf-core/bcftools/reheader/** @bjohnnyd @jemten @ramprasadn
-modules/nf-core/bcftools/roh/** @ramprasadn
-modules/nf-core/bcftools/sort/** @Gwennid
-modules/nf-core/bcftools/split/** @matthdsm @atrigila
-modules/nf-core/bcftools/stats/** @joseespinosa @drpatelh @SusiJo @TCLamnidis
-modules/nf-core/bcftools/view/** @abhi18av
-modules/nf-core/bcl2fastq/** @matthdsm
-modules/nf-core/bclconvert/** @matthdsm
-modules/nf-core/beagle5/beagle/** @ashotmarg
-modules/nf-core/bedtools/bamtobed/** @yuukiiwa @drpatelh
-modules/nf-core/bedtools/closest/** @nvnieuwk
-modules/nf-core/bedtools/complement/** @edmundmiller @sruthipsuresh @drpatelh
-modules/nf-core/bedtools/coverage/** @priyanka-surana
-modules/nf-core/bedtools/genomecov/** @edmundmiller @sruthipsuresh @drpatelh @sidorov-si @chris-cheshire
-modules/nf-core/bedtools/getfasta/** @joseespinosa @drpatelh
-modules/nf-core/bedtools/groupby/** @mashehu
-modules/nf-core/bedtools/intersect/** @edmundmiller @sruthipsuresh @drpatelh @sidorov-si
-modules/nf-core/bedtools/jaccard/** @nvnieuwk
-modules/nf-core/bedtools/makewindows/** @kevbrick @nvnieuwk
-modules/nf-core/bedtools/map/** @ekushele
-modules/nf-core/bedtools/maskfasta/** @joseespinosa @drpatelh
-modules/nf-core/bedtools/merge/** @edmundmiller @sruthipsuresh @drpatelh
-modules/nf-core/bedtools/multiinter/** @matthdsm
-modules/nf-core/bedtools/shift/** @ekushele
-modules/nf-core/bedtools/slop/** @edmundmiller @sruthipsuresh @drpatelh
-modules/nf-core/bedtools/sort/** @edmundmiller @sruthipsuresh @drpatelh @chris-cheshire @adamrtalbot
-modules/nf-core/bedtools/split/** @nvnieuwk
-modules/nf-core/bedtools/subtract/** @sidorov-si
-modules/nf-core/bedtools/unionbedg/** @ekushele
-modules/nf-core/bioawk/** @jfy133
-modules/nf-core/biobambam/bammarkduplicates2/** @muffato
-modules/nf-core/biobambam/bammerge/** @matthdsm
-modules/nf-core/biobambam/bamsormadup/** @matthdsm
-modules/nf-core/biohansel/** @rpetit3
-modules/nf-core/biscuit/align/** @njspix
-modules/nf-core/biscuit/biscuitblaster/** @njspix
-modules/nf-core/biscuit/bsconv/** @njspix
-modules/nf-core/biscuit/epiread/** @njspix
-modules/nf-core/biscuit/index/** @njspix
-modules/nf-core/biscuit/mergecg/** @njspix
-modules/nf-core/biscuit/pileup/** @njspix
-modules/nf-core/biscuit/qc/** @njspix
-modules/nf-core/biscuit/vcf2bed/** @njspix
-modules/nf-core/bismark/align/** @phue @FelixKrueger @ewels
-modules/nf-core/bismark/coverage2cytosine/** @FelixKrueger @ewels
-modules/nf-core/bismark/deduplicate/** @phue @FelixKrueger @ewels
-modules/nf-core/bismark/genomepreparation/** @phue @FelixKrueger @ewels
-modules/nf-core/bismark/methylationextractor/** @phue @FelixKrueger @ewels
-modules/nf-core/bismark/report/** @phue @FelixKrueger @ewels
-modules/nf-core/bismark/summary/** @phue @FelixKrueger @ewels
-modules/nf-core/blast/blastn/** @joseespinosa @drpatelh @vagkaratzas
-modules/nf-core/blast/blastp/** @vagkaratzas
-modules/nf-core/blast/makeblastdb/** @joseespinosa @drpatelh @vagkaratzas
-modules/nf-core/blast/tblastn/** @yumisims @gq2 @vagkaratzas
-modules/nf-core/blat/** @d-jch
-modules/nf-core/bowtie2/align/** @joseespinosa @drpatelh
-modules/nf-core/bowtie2/build/** @joseespinosa @drpatelh
-modules/nf-core/bowtie/align/** @kevinmenden
-modules/nf-core/bowtie/build/** @kevinmenden @drpatelh
-modules/nf-core/bracken/bracken/** @Midnighter
-modules/nf-core/bracken/combinebrackenoutputs/** @jfy133
-modules/nf-core/busco/** @priyanka-surana @charles-plessy @mahesh-panchal @muffato @jvhagey
-modules/nf-core/bwa/aln/** @jfy133
-modules/nf-core/bwa/index/** @drpatelh @maxulysse
-modules/nf-core/bwamem2/index/** @maxulysse
-modules/nf-core/bwamem2/mem/** @maxulysse
-modules/nf-core/bwa/mem/** @drpatelh @jeremy1805
-modules/nf-core/bwameth/align/** @phue
-modules/nf-core/bwameth/index/** @phue
-modules/nf-core/bwa/sampe/** @jfy133
-modules/nf-core/bwa/samse/** @jfy133
-modules/nf-core/cadd/** @ramprasadn
-modules/nf-core/calder2/** @lucananni93
-modules/nf-core/canu/** @scorreard
-modules/nf-core/cat/cat/** @erikrikarddaniel @FriederikeHanssen
-modules/nf-core/cat/fastq/** @joseespinosa @drpatelh
-modules/nf-core/cdhit/cdhitest/** @Joon-Klaps
-modules/nf-core/cdhit/cdhit/** @timslittle
-modules/nf-core/cellpose/** @josenimo
-modules/nf-core/cellrangeratac/count/** @ggabernet @edmundmiller @heylf
-modules/nf-core/cellrangeratac/mkfastq/** @ggabernet @edmundmiller @RHReynolds @heylf
-modules/nf-core/cellrangeratac/mkref/** @ggabernet @heylf
-modules/nf-core/cellranger/count/** @ggabernet @edmundmiller
-modules/nf-core/cellranger/mkfastq/** @ggabernet @edmundmiller @RHReynolds
-modules/nf-core/cellranger/mkgtf/** @ggabernet @edmundmiller
-modules/nf-core/cellranger/mkref/** @ggabernet
-modules/nf-core/cellranger/mkvdjref/** @ggabernet @klkeys
-modules/nf-core/cellranger/multi/** @klkeys
-modules/nf-core/cellranger/vdj/** @ggabernet @edmundmiller @klkeys
-modules/nf-core/centrifuge/centrifuge/** @sofstam @jfy133 @sateeshperi
-modules/nf-core/centrifuge/kreport/** @sofstam @jfy133
-modules/nf-core/checkm/lineagewf/** @jfy133
-modules/nf-core/checkm/qa/** @jfy133
-modules/nf-core/checkv/downloaddatabase/** @Joon-Klaps
-modules/nf-core/checkv/endtoend/** @Joon-Klaps
-modules/nf-core/checkv/updatedatabase/** @Joon-Klaps
-modules/nf-core/chopper/** @FynnFreyer
-modules/nf-core/chromap/chromap/** @mahesh-panchal @joseespinosa
-modules/nf-core/chromap/index/** @mahesh-panchal @joseespinosa
-modules/nf-core/chromograph/** @ramprasadn
-modules/nf-core/circexplorer2/annotate/** @BarryDigby
-modules/nf-core/circexplorer2/parse/** @BarryDigby
-modules/nf-core/clippy/** @marc-jones @CharlotteAnne
-modules/nf-core/clonalframeml/** @rpetit3
-modules/nf-core/clustalo/align/** @luisas
-modules/nf-core/clustalo/guidetree/** @luisas
-modules/nf-core/cmseq/polymut/** @maxibor
-modules/nf-core/cnvkit/access/** @adamrtalbot @priesgo
-modules/nf-core/cnvkit/antitarget/** @adamrtalbot @priesgo @SusiJo
-modules/nf-core/cnvkit/batch/** @adamrtalbot @drpatelh @fbdtemme @kaurravneet4123 @KevinMenden @lassefolkersen @MaxUlysse @priesgo @SusiJo
-modules/nf-core/cnvkit/call/** @adamrtalbot @priesgo
-modules/nf-core/cnvkit/export/** @adamrtalbot @priesgo
-modules/nf-core/cnvkit/genemetrics/** @adamrtalbot @marrip @priesgo
-modules/nf-core/cnvkit/reference/** @adamrtalbot @priesgo @SusiJo
-modules/nf-core/cnvkit/target/** @adamrtalbot @priesgo
-modules/nf-core/cnvnator/cnvnator/** @ramprasadn
-modules/nf-core/cnvnator/convert2vcf/** @ramprasadn
-modules/nf-core/cnvpytor/callcnvs/** @sima-r
-modules/nf-core/cnvpytor/histogram/** @sima-r @ramprasadn
-modules/nf-core/cnvpytor/importreaddepth/** @sima-r @ramprasadn
-modules/nf-core/cnvpytor/partition/** @sima-r @ramprasadn
-modules/nf-core/cnvpytor/view/** @sima-r @ramprasadn
-modules/nf-core/concoct/concoctcoveragetable/** @jfy133
-modules/nf-core/concoct/concoct/** @jfy133
-modules/nf-core/concoct/cutupfasta/** @jfy133
-modules/nf-core/concoct/extractfastabins/** @jfy133
-modules/nf-core/concoct/mergecutupclustering/** @jfy133
-modules/nf-core/conifer/** @icaromsc @rpetit3
-modules/nf-core/controlfreec/assesssignificance/** @FriederikeHanssen
-modules/nf-core/controlfreec/freec2bed/** @FriederikeHanssen
-modules/nf-core/controlfreec/freec2circos/** @FriederikeHanssen
-modules/nf-core/controlfreec/freec/** @FriederikeHanssen
-modules/nf-core/controlfreec/makegraph/** @FriederikeHanssen
-modules/nf-core/cooler/balance/** @nservant @muffato
-modules/nf-core/cooler/cload/** @jianhong @muffato
-modules/nf-core/cooler/digest/** @jianhong
-modules/nf-core/cooler/dump/** @jianhong @muffato
-modules/nf-core/cooler/makebins/** @nservant @muffato
-modules/nf-core/cooler/merge/** @jianhong
-modules/nf-core/cooler/zoomify/** @jianhong
-modules/nf-core/coreograph/** @arozhada @MargotCh
-modules/nf-core/crisprcleanr/normalize/** @LaurenceKuhl
-modules/nf-core/crumble/** @priyanka-surana
-modules/nf-core/csvtk/concat/** @rpetit3
-modules/nf-core/csvtk/join/** @anoronh4
-modules/nf-core/csvtk/split/** @SusiJo
-modules/nf-core/custom/dumpsoftwareversions/** @drpatelh @grst
-modules/nf-core/custom/getchromsizes/** @tamara-hodgetts @chris-cheshire @muffato
-modules/nf-core/custom/matrixfilter/** @pinin4fjords
-modules/nf-core/custom/sratoolsncbisettings/** @Midnighter
-modules/nf-core/custom/tabulartogseacls/** @pinin4fjords
-modules/nf-core/custom/tabulartogseagct/** @pinin4fjords
-modules/nf-core/cutadapt/** @drpatelh @kevinmenden
-modules/nf-core/cutesv/** @christopher-hakkaart @yuukiiwa
-modules/nf-core/damageprofiler/** @jfy133
-modules/nf-core/dastool/dastool/** @maxibor @jfy133
-modules/nf-core/dastool/fastatocontig2bin/** @maxibor @jfy133
-modules/nf-core/dastool/scaffolds2bin/** @maxibor
-modules/nf-core/dedup/** @jfy133
-modules/nf-core/deeparg/downloaddata/** @jfy133
-modules/nf-core/deeparg/predict/** @jfy133
-modules/nf-core/deepbgc/download/** @louperelo
-modules/nf-core/deepbgc/pipeline/** @louperelo @jfy133
-modules/nf-core/deepcell/mesmer/** @migueLib @chiarasch
-modules/nf-core/deeptmhmm/** @vagkaratzas
-modules/nf-core/deeptools/bamcoverage/** @FriederikeHanssen @SusiJo
-modules/nf-core/deeptools/computematrix/** @jeremy1805 @edmundmiller @drpatelh @joseespinosa
-modules/nf-core/deeptools/multibamsummary/** @tamara-hodgetts @chris-cheshire
-modules/nf-core/deeptools/plotcorrelation/** @tamara-hodgetts @chris-cheshire
-modules/nf-core/deeptools/plotfingerprint/** @edmundmiller @drpatelh @joseespinosa
-modules/nf-core/deeptools/plotheatmap/** @edmundmiller @drpatelh @joseespinosa
-modules/nf-core/deeptools/plotpca/** @tamara-hodgetts @chris-cheshire
-modules/nf-core/deeptools/plotprofile/** @edmundmiller @drpatelh @joseespinosa
-modules/nf-core/deepvariant/** @abhi18av @ramprasadn
-modules/nf-core/delly/call/** @projectoriented @nvnieuwk
-modules/nf-core/deseq2/differential/** @pinin4fjords
-modules/nf-core/diamond/blastp/** @spficklin @jfy133
-modules/nf-core/diamond/blastx/** @spficklin @jfy133 @mjamy
-modules/nf-core/diamond/makedb/** @spficklin
-modules/nf-core/dragmap/align/** @edmundmiller
-modules/nf-core/dragmap/hashtable/** @edmundmiller
-modules/nf-core/dragonflye/** @rpetit3
-modules/nf-core/dshbio/exportsegments/** @heuermh
-modules/nf-core/dshbio/filterbed/** @heuermh
-modules/nf-core/dshbio/filtergff3/** @heuermh
-modules/nf-core/dshbio/splitbed/** @heuermh
-modules/nf-core/dshbio/splitgff3/** @heuermh
-modules/nf-core/duphold/** @nvnieuwk
-modules/nf-core/ectyper/** @rpetit3
-modules/nf-core/eido/convert/** @rafalstepien
-modules/nf-core/eido/validate/** @rafalstepien
-modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/** @TCLamnidis
-modules/nf-core/eklipse/** @Lucpen
-modules/nf-core/elprep/filter/** @matthdsm
-modules/nf-core/elprep/merge/** @matthdsm
-modules/nf-core/elprep/split/** @matthdsm
-modules/nf-core/emboss/cons/** @Joon-Klaps
-modules/nf-core/emboss/revseq/** @erikrikarddaniel
-modules/nf-core/emboss/seqret/** @MillironX
-modules/nf-core/emmtyper/** @rpetit3
-modules/nf-core/endorspy/** @aidaanva
-modules/nf-core/ensemblvep/download/** @maxulysse
-modules/nf-core/ensemblvep/filtervep/** @ramprasadn
-modules/nf-core/ensemblvep/vep/** @maxulysse @matthdsm @nvnieuwk
-modules/nf-core/entrezdirect/esearch/** @alxndrdiaz
-modules/nf-core/entrezdirect/esummary/** @alxndrdiaz
-modules/nf-core/entrezdirect/xtract/** @alxndrdiaz
-modules/nf-core/epang/place/** @erikrikarddaniel
-modules/nf-core/epang/split/** @erikrikarddaniel
-modules/nf-core/expansionhunterdenovo/merge/** @nvnieuwk
-modules/nf-core/expansionhunterdenovo/profile/** @nvnieuwk
-modules/nf-core/expansionhunter/** @jemten
-modules/nf-core/falco/** @lucacozzuto
-modules/nf-core/famsa/align/** @luisas
-modules/nf-core/famsa/guidetree/** @luisas
-modules/nf-core/faqcs/** @mjcipriano @sateeshperi @hseabolt
-modules/nf-core/fargene/** @louperelo
-modules/nf-core/fastani/** @abhi18av
-modules/nf-core/fastawindows/** @muffato
-modules/nf-core/fastk/fastk/** @mahesh-panchal
-modules/nf-core/fastk/histex/** @mahesh-panchal
-modules/nf-core/fastk/merge/** @mahesh-panchal
-modules/nf-core/fastp/** @drpatelh @kevinmenden
-modules/nf-core/fastqc/** @drpatelh @grst @FelixKrueger
-modules/nf-core/fastqscan/** @rpetit3
-modules/nf-core/fasttree/** @aunderwo
-modules/nf-core/fcs/fcsadaptor/** @d4straub
-modules/nf-core/fcs/fcsgx/** @tillenglert
-modules/nf-core/ffq/** @drpatelh
-modules/nf-core/fgbio/callduplexconsensusreads/** @lescai
-modules/nf-core/fgbio/callmolecularconsensusreads/** @sruthipsuresh
-modules/nf-core/fgbio/fastqtobam/** @lescai @matthdsm
-modules/nf-core/fgbio/filterconsensusreads/** @lescai
-modules/nf-core/fgbio/groupreadsbyumi/** @lescai
-modules/nf-core/fgbio/sortbam/** @sruthipsuresh
-modules/nf-core/fgbio/zipperbams/** @lescai
-modules/nf-core/filtlong/** @d4straub @sofstam
-modules/nf-core/flash/** @Erkison
-modules/nf-core/flye/** @mirpedrol
-modules/nf-core/fq/generate/** @adamrtalbot
-modules/nf-core/fq/lint/** @adamrtalbot
-modules/nf-core/fq/subsample/** @adamrtalbot
-modules/nf-core/fqtk/** @nh13 @sam-white04
-modules/nf-core/freebayes/** @maxibor @FriederikeHanssen @maxulysse
-modules/nf-core/freyja/boot/** @Joon-Klaps
-modules/nf-core/freyja/demix/** @Joon-Klaps
-modules/nf-core/freyja/update/** @Joon-Klaps
-modules/nf-core/freyja/variants/** @Joon-Klaps
-modules/nf-core/galah/** @prototaxites
-modules/nf-core/gamma/gamma/** @sateeshperi @rastanton @jvhagey
-modules/nf-core/gangstr/** @nvnieuwk
-modules/nf-core/ganon/buildcustom/** @jfy133
-modules/nf-core/ganon/classify/** @jfy133
-modules/nf-core/ganon/report/** @jfy133
-modules/nf-core/ganon/table/** @jfy133
-modules/nf-core/gappa/examineassign/** @erikrikarddaniel
-modules/nf-core/gappa/examinegraft/** @erikrikarddaniel
-modules/nf-core/gappa/examineheattree/** @erikrikarddaniel
-modules/nf-core/gatk4/annotateintervals/** @nvnieuwk
-modules/nf-core/gatk4/applybqsrspark/** @yocra3 @FriederikeHanssen @maxulysse
-modules/nf-core/gatk4/applybqsr/** @yocra3 @FriederikeHanssen
-modules/nf-core/gatk4/applyvqsr/** @GCJMackenzie
-modules/nf-core/gatk4/asereadcounter/** @Lucpen
-modules/nf-core/gatk4/baserecalibratorspark/** @yocra3 @FriederikeHanssen @maxulysse
-modules/nf-core/gatk4/baserecalibrator/** @yocra3 @FriederikeHanssen @maxulysse
-modules/nf-core/gatk4/bedtointervallist/** @kevinmenden @ramprasadn
-modules/nf-core/gatk4/calculatecontamination/** @GCJMackenzie @maxulysse
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-modules/nf-core/gatk4/combinegvcfs/** @sateeshperi @mjcipriano @hseabolt @maxulysse
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-modules/nf-core/gatk4/denoisereadcounts/** @ramprasadn
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-modules/nf-core/gatk4/filterintervals/** @ryanjameskennedy @ViktorHy
-modules/nf-core/gatk4/filtermutectcalls/** @GCJMackenzie @maxulysse @ramprasadn
-modules/nf-core/gatk4/filtervarianttranches/** @FriederikeHanssen
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-modules/nf-core/gatk4/gatherpileupsummaries/** @FriederikeHanssen @maxulysse
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-modules/nf-core/gatk4/genotypegvcfs/** @santiagorevale @maxulysse
-modules/nf-core/gatk4/germlinecnvcaller/** @ryanjameskennedy @ViktorHy
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-modules/nf-core/gatk4/haplotypecaller/** @suzannejin @FriederikeHanssen
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-modules/nf-core/gatk4/intervallisttobed/** @FriederikeHanssen
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-modules/nf-core/gatk4/mergemutectstats/** @FriederikeHanssen
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-modules/nf-core/gatk4/mutect2/** @GCJMackenzie @ramprasadn
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-modules/nf-core/gatk4/preprocessintervals/** @ryanjameskennedy @ViktorHy @ramprasadn
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-modules/nf-core/gatk4/printsvevidence/** @nvnieuwk
-modules/nf-core/gatk4/reblockgvcf/** @nvnieuwk
-modules/nf-core/gatk4/revertsam/** @kevinmenden
-modules/nf-core/gatk4/samtofastq/** @kevinmenden
-modules/nf-core/gatk4/selectvariants/** @mjcipriano @ramprasadn
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-modules/nf-core/gatk4/sitedepthtobaf/** @nvnieuwk
-modules/nf-core/gatk4/splitcram/** @nvnieuwk
-modules/nf-core/gatk4/splitintervals/** @nvnieuwk @ramprasadn
-modules/nf-core/gatk4/splitncigarreads/** @kevinmenden
-modules/nf-core/gatk4/svannotate/** @nvnieuwk
-modules/nf-core/gatk4/svcluster/** @nvnieuwk
-modules/nf-core/gatk4/variantfiltration/** @kevinmenden @ramprasadn
-modules/nf-core/gatk4/variantrecalibrator/** @GCJMackenzie @nickhsmith
-modules/nf-core/gatk/indelrealigner/** @jfy133
-modules/nf-core/gatk/realignertargetcreator/** @jfy133
-modules/nf-core/gatk/unifiedgenotyper/** @ilight1542 @jfy133
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-modules/nf-core/gem3/gem3indexer/** @miqalvarez
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-modules/nf-core/genmap/index/** @jianhong @nvnieuwk
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-modules/nf-core/genomad/download/** @CarsonJM
-modules/nf-core/genomad/endtoend/** @CarsonJM
-modules/nf-core/genomescope2/** @mahesh-panchal
-modules/nf-core/genotyphi/parse/** @rpetit3
-modules/nf-core/genrich/** @JoseEspinosa @samuelruizperez
-modules/nf-core/geoquery/getgeo/** @azedinez @pinin4fjords
-modules/nf-core/gfaffix/** @heuermh
-modules/nf-core/gfastats/** @mahesh-panchal
-modules/nf-core/gfatools/gfa2fa/** @mahesh-panchal
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-modules/nf-core/gffcompare/** @jemten
-modules/nf-core/gffread/** @edmundmiller
-modules/nf-core/gget/gget/** @adamrtalbot
-modules/nf-core/glimpse2/chunk/** @louislenezet
-modules/nf-core/glimpse2/concordance/** @louislenezet
-modules/nf-core/glimpse2/ligate/** @louislenezet
-modules/nf-core/glimpse2/phase/** @LouisLeNezet
-modules/nf-core/glimpse2/splitreference/** @LouisLeNezet
-modules/nf-core/glimpse/chunk/** @louislenezet
-modules/nf-core/glimpse/concordance/** @louislenezet
-modules/nf-core/glimpse/ligate/** @louislenezet
-modules/nf-core/glimpse/phase/** @louislenezet
-modules/nf-core/glimpse/sample/** @louislenezet
-modules/nf-core/glnexus/** @ramprasadn
-modules/nf-core/gnu/sort/** @DLBPointon
-modules/nf-core/goat/taxonsearch/** @alxndrdiaz @muffato
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-modules/nf-core/goleft/indexsplit/** @matthdsm
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-modules/nf-core/graphtyper/vcfconcatenate/** @zachary-foster
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-modules/nf-core/gstama/polyacleanup/** @sguizard
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-modules/nf-core/gunzip/** @joseespinosa @drpatelh @jfy133
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-modules/nf-core/hamronization/abricate/** @jasmezz
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-modules/nf-core/hicexplorer/hicpca/** @jianhong
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-modules/nf-core/hisat2/align/** @ntoda03 @ramprasadn
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-modules/nf-core/hisat2/extractsplicesites/** @ntoda03 @ramprasadn
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-modules/nf-core/hmmcopy/generatemap/** @sppearce @adamrtalbot
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-modules/nf-core/hmmer/eslalimask/** @erikrikarddaniel
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-modules/nf-core/hmmer/hmmalign/** @erikrikarddaniel @jfy133
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-modules/nf-core/hmmer/hmmsearch/** @Midnighter
-modules/nf-core/hmtnote/annotate/** @sysbiocoder
-modules/nf-core/homer/annotatepeaks/** @drpatelh @kevinmenden
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-modules/nf-core/icountmini/summary/** @marc-jones @chris-cheshire @charlotteanne
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-modules/nf-core/ismapper/** @rpetit3
-modules/nf-core/isoseq3/cluster/** @sguizard
-modules/nf-core/isoseq3/refine/** @sguizard
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-modules/nf-core/jupyternotebook/** @grst
-modules/nf-core/kaiju/kaiju2krona/** @MillironX
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-modules/nf-core/kaiju/kaiju/** @talnor @sofstam @jfy133
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-modules/nf-core/khmer/uniquekmers/** @JoseEspinosa
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-modules/nf-core/krakentools/combinekreports/** @jfy133
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-modules/nf-core/paragraph/idxdepth/** @nvnieuwk
-modules/nf-core/paragraph/multigrmpy/** @nvnieuwk
-modules/nf-core/paragraph/vcf2paragraph/** @nvnieuwk
-modules/nf-core/pasty/** @rpetit3
-modules/nf-core/pbbam/pbmerge/** @sguizard
-modules/nf-core/pbccs/** @sguizard
-modules/nf-core/pbptyper/** @rpetit3
-modules/nf-core/pear/** @mirpedrol
-modules/nf-core/peddy/** @rannick
-modules/nf-core/peka/** @kkuret @codeprimate123 @chris-cheshire @charlotteanne
-modules/nf-core/phantompeakqualtools/** @drpatelh @edmundmiller @JoseEspinosa
-modules/nf-core/phispy/** @jvfe
-modules/nf-core/phyloflash/** @abhi18av
-modules/nf-core/picard/addorreplacereadgroups/** @sateeshperi @mjcipriano @hseabolt @cmatKhan @muffato
-modules/nf-core/picard/bedtointervallist/** @kevinmenden @matthdsm
-modules/nf-core/picard/cleansam/** @sateeshperi @mjcipriano @hseabolt
-modules/nf-core/picard/collecthsmetrics/** @projectoriented @matthdsm
-modules/nf-core/picard/collectinsertsizemetrics/** @FerriolCalvet
-modules/nf-core/picard/collectmultiplemetrics/** @drpatelh
-modules/nf-core/picard/collectrnaseqmetrics/** @anoronh4
-modules/nf-core/picard/collectwgsmetrics/** @drpatelh @flowuenne @lassefolkersen @ramprasadn
-modules/nf-core/picard/createsequencedictionary/** @sateeshperi @mjcipriano @hseabolt
-modules/nf-core/picard/crosscheckfingerprints/** @matthdsm
-modules/nf-core/picard/fastqtosam/** @matthdsm
-modules/nf-core/picard/filtersamreads/** @jfy133
-modules/nf-core/picard/fixmateinformation/** @sateeshperi @mjcipriano @hseabolt
-modules/nf-core/picard/liftovervcf/** @lucpen @ramprasadn
-modules/nf-core/picard/markduplicates/** @drpatelh @projectoriented @ramprasadn
-modules/nf-core/picard/mergesamfiles/** @drpatelh
-modules/nf-core/picard/renamesampleinvcf/** @Lucpen
-modules/nf-core/picard/scatterintervalsbyns/** @nvnieuwk
-modules/nf-core/picard/sortsam/** @jfy133
-modules/nf-core/picard/sortvcf/** @ramprasadn
-modules/nf-core/pilon/** @scorreard
-modules/nf-core/pindel/pindel/** @marrip
+.github/workflows/** @nf-core/a-team
+tests/config @nf-core/a-team
+
+# Opt-in
+modules/nf-core/bedtools/** @edmundmiller
+modules/nf-core/dragmap/** @edmundmiller
+modules/nf-core/ensemblvep/** @maxulysse
+modules/nf-core/gatk4/** @maxulysse
+modules/nf-core/homer/** @edmundmiller
+modules/nf-core/snpeff/** @maxulysse
 modules/nf-core/pints/caller/** @edmundmiller
-modules/nf-core/pirate/** @rpetit3
-modules/nf-core/plasmidfinder/** @rpetit3
-modules/nf-core/plasmidid/** @joseespinosa @drpatelh
-modules/nf-core/platypus/** @kubranarci
-modules/nf-core/plink2/extract/** @nebfield
-modules/nf-core/plink2/score/** @nebfield
-modules/nf-core/plink2/vcf/** @nebfield
-modules/nf-core/plink/bcf/** @atrigila
-modules/nf-core/plink/exclude/** @atrigila
-modules/nf-core/plink/extract/** @nebfield
-modules/nf-core/plink/indep/** @atrigila
-modules/nf-core/plink/indeppairwise/** @atrigila
-modules/nf-core/plink/recode/** @atrigila
-modules/nf-core/plink/vcf/** @Mxrcon @abhi18av
-modules/nf-core/pmdtools/filter/** @alexandregilardet
-modules/nf-core/pneumocat/** @rpetit3
-modules/nf-core/porechop/abi/** @sofstam
-modules/nf-core/porechop/porechop/** @ggabernet @jasmezz @d4straub @LaurenceKuhl @SusiJo @jonasscheid @jonoave @GokceOGUZ @jfy133
-modules/nf-core/preseq/ccurve/** @drpatelh @edmundmiller
-modules/nf-core/preseq/lcextrap/** @drpatelh @edmundmiller
-modules/nf-core/pretextmap/** @marrip @getrudeln
-modules/nf-core/pretextsnapshot/** @epaule
-modules/nf-core/prinseqplusplus/** @jfy133
-modules/nf-core/prodigal/** @grst
-modules/nf-core/prokka/** @rpetit3
-modules/nf-core/propr/logratio/** @suzannejin @oprana22
-modules/nf-core/propr/propd/** @suzannejin
-modules/nf-core/proteus/readproteingroups/** @WackerO
-modules/nf-core/pureclip/** @charlotteanne @marcjones
-modules/nf-core/purecn/coverage/** @aldosr @lbeltrame
-modules/nf-core/purecn/intervalfile/** @aldosr @lbeltrame
-modules/nf-core/purecn/normaldb/** @aldosr @lbeltrame
-modules/nf-core/purecn/run/** @aldosr @lbeltrame
-modules/nf-core/purgedups/calcuts/** @mahesh-panchal
-modules/nf-core/purgedups/getseqs/** @mahesh-panchal
-modules/nf-core/purgedups/histplot/** @mahesh-panchal
-modules/nf-core/purgedups/pbcstat/** @mahesh-panchal
-modules/nf-core/purgedups/purgedups/** @mahesh-panchal
-modules/nf-core/purgedups/splitfa/** @mahesh-panchal
-modules/nf-core/pycoqc/** @joseespinosa @drpatelh
-modules/nf-core/pydamage/analyze/** @maxibor
-modules/nf-core/pydamage/filter/** @maxibor
-modules/nf-core/pyrodigal/** @louperelo
-modules/nf-core/qcat/** @yuukiiwa @drpatelh
-modules/nf-core/qualimap/bamqccram/** @FriederikeHanssen
-modules/nf-core/qualimap/bamqc/** @phue
-modules/nf-core/qualimap/rnaseq/** @FriederikeHanssen
-modules/nf-core/quast/** @drpatelh @kevinmenden
-modules/nf-core/quilt/quilt/** @atrigila
-modules/nf-core/racon/** @avantonder
-modules/nf-core/rapidnj/** @aunderwo @avantonder
-modules/nf-core/rasusa/** @thanhleviet
-modules/nf-core/raven/** @fmalmeida
-modules/nf-core/raxmlng/** @avantonder @aunderwo
-modules/nf-core/rgi/main/** @rpetit3 @jfy133
-modules/nf-core/rhocall/annotate/** @ramprasadn
-modules/nf-core/rmarkdownnotebook/** @grst
-modules/nf-core/roary/** @rpetit3
-modules/nf-core/rsem/calculateexpression/** @drpatelh @kevinmenden
-modules/nf-core/rsem/preparereference/** @drpatelh @kevinmenden
-modules/nf-core/rseqc/bamstat/** @drpatelh @kevinmenden
-modules/nf-core/rseqc/inferexperiment/** @drpatelh @kevinmenden
-modules/nf-core/rseqc/innerdistance/** @drpatelh @kevinmenden
-modules/nf-core/rseqc/junctionannotation/** @drpatelh @kevinmenden
-modules/nf-core/rseqc/junctionsaturation/** @drpatelh @kevinmenden
-modules/nf-core/rseqc/readdistribution/** @drpatelh @kevinmenden
-modules/nf-core/rseqc/readduplication/** @drpatelh @kevinmenden
-modules/nf-core/rseqc/tin/** @drpatelh
-modules/nf-core/rtgtools/format/** @nvnieuwk
-modules/nf-core/rtgtools/pedfilter/** @nvnieuwk
-modules/nf-core/rtgtools/rocplot/** @nvnieuwk
-modules/nf-core/rtgtools/vcfeval/** @nvnieuwk
-modules/nf-core/salmon/index/** @kevinmenden @drpatelh
-modules/nf-core/salmon/quant/** @kevinmenden @drpatelh
-modules/nf-core/salsa2/** @scorreard
-modules/nf-core/sam2lca/analyze/** @maxibor
-modules/nf-core/sambamba/flagstat/** @kubranarci
-modules/nf-core/sambamba/markdup/** @BioInf2305
-modules/nf-core/samblaster/** @lescai
-modules/nf-core/samtools/ampliconclip/** @bjohnnyd
-modules/nf-core/samtools/bam2fq/** @lescai
-modules/nf-core/samtools/calmd/** @JackCurragh
-modules/nf-core/samtools/cat/** @matthdsm
-modules/nf-core/samtools/collatefastq/** @lescai @maxulysse @matthdsm
-modules/nf-core/samtools/collate/** @priyanka-surana
-modules/nf-core/samtools/convert/** @FriederikeHanssen @maxulysse
-modules/nf-core/samtools/coverage/** @LouisLeNezet
-modules/nf-core/samtools/depth/** @louperelo @nevinwu
-modules/nf-core/samtools/dict/** @muffato
-modules/nf-core/samtools/faidx/** @drpatelh @phue
-modules/nf-core/samtools/fasta/** @priyanka-surana
-modules/nf-core/samtools/fastq/** @priyanka-surana @suzannejin
-modules/nf-core/samtools/fixmate/** @sppearce
-modules/nf-core/samtools/flagstat/** @drpatelh
-modules/nf-core/samtools/getrg/** @matthdsm
-modules/nf-core/samtools/idxstats/** @drpatelh
-modules/nf-core/samtools/import/** @matthdsm
-modules/nf-core/samtools/index/** @drpatelh @maxulysse
-modules/nf-core/samtools/markdup/** @priyanka-surana
-modules/nf-core/samtools/merge/** @drpatelh @yuukiiwa @maxulysse @FriederikeHanssen @ramprasadn
-modules/nf-core/samtools/mpileup/** @drpatelh @joseespinosa
-modules/nf-core/samtools/reheader/** @louislenezet
-modules/nf-core/samtools/sort/** @drpatelh
-modules/nf-core/samtools/stats/** @drpatelh @FriederikeHanssen @ramprasadn
-modules/nf-core/samtools/view/** @drpatelh @joseespinosa @FriederikeHanssen @priyanka-surana
-modules/nf-core/scimap/mcmicro/** @luiskuhn
-modules/nf-core/scoary/** @rpetit3
-modules/nf-core/scramble/clusteranalysis/** @nvnieuwk
-modules/nf-core/scramble/clusteridentifier/** @nvnieuwk
-modules/nf-core/seacr/callpeak/** @chris-cheshire
-modules/nf-core/segemehl/align/** @BarryDigby
-modules/nf-core/segemehl/index/** @BarryDigby
-modules/nf-core/semibin/singleeasybin/** @BigDataBiology
-modules/nf-core/sentieon/** @DonFreed
-modules/nf-core/sentieon/applyvarcal/** @assp8200
-modules/nf-core/sentieon/bwaindex/** @drpatelh @maxulysse
-modules/nf-core/sentieon/bwamem/** @asp8200
-modules/nf-core/sentieon/datametrics/** @ramprasadn
-modules/nf-core/sentieon/dedup/** @asp8200
-modules/nf-core/sentieon/dnamodelapply/** @ramprasadn
-modules/nf-core/sentieon/dnascope/** @ramprasadn
-modules/nf-core/sentieon/gvcftyper/** @asp8200
-modules/nf-core/sentieon/haplotyper/** @asp8200
-modules/nf-core/sentieon/readwriter/** @ramprasadn
-modules/nf-core/sentieon/tnhaplotyper2/** @asp8200
-modules/nf-core/sentieon/tnscope/** @ramprasadn
-modules/nf-core/sentieon/varcal/** @asp8200
-modules/nf-core/sentieon/wgsmetrics/** @ramprasadn
-modules/nf-core/seqkit/fx2tab/** @heuermh
-modules/nf-core/seqkit/grep/** @Joon-Klaps
-modules/nf-core/seqkit/pair/** @sateeshperi @mjcipriano @hseabolt
-modules/nf-core/seqkit/replace/** @mjcipriano
-modules/nf-core/seqkit/sliding/** @DLBPointon
-modules/nf-core/seqkit/split2/** @FriederikeHanssen
-modules/nf-core/seqkit/stats/** @Midnighter
-modules/nf-core/seqkit/tab2fx/** @heuermh
-modules/nf-core/seqsero2/** @rpetit3
-modules/nf-core/seqtk/cutn/** @DLBPointon
-modules/nf-core/seqtk/mergepe/** @emnilsson
-modules/nf-core/seqtk/rename/** @hseabolt @mjcipriano @sateeshperi
-modules/nf-core/seqtk/sample/** @kaurravneet4123 @sidorov-si @adamrtalbot
-modules/nf-core/seqtk/seq/** @hseabolt @mjcipriano @sateeshperi
-modules/nf-core/seqtk/subseq/** @sidorov-si
-modules/nf-core/sequencetools/pileupcaller/** @TCLamnidis
-modules/nf-core/sequenzautils/bam2seqz/** @kaurravneet4123
-modules/nf-core/sequenzautils/gcwiggle/** @kaurravneet4123
-modules/nf-core/seqwish/induce/** @heuermh
-modules/nf-core/seroba/run/** @rpetit3
-modules/nf-core/sexdeterrmine/** @TCLamnidis
-modules/nf-core/sgdemux/** @nh13 @sam-white04
-modules/nf-core/shapeit5/ligate/** @louislenezet
-modules/nf-core/shapeit5/phasecommon/** @LouisLeNezet
-modules/nf-core/shapeit5/phaserare/** @LouisLeNezet
-modules/nf-core/shapeit5/switch/** @LouisLeNezet
-modules/nf-core/shasta/** @fmalmeida
-modules/nf-core/shasum/** @matthdsm
-modules/nf-core/shigatyper/** @rpetit3
-modules/nf-core/shigeifinder/** @rpetit3
-modules/nf-core/shinyngs/app/** @pinin4fjords
-modules/nf-core/shinyngs/staticdifferential/** @pinin4fjords
-modules/nf-core/shinyngs/staticexploratory/** @pinin4fjords
-modules/nf-core/shinyngs/validatefomcomponents/** @pinin4fjords
-modules/nf-core/shovill/** @rpetit3
-modules/nf-core/sickle/** @BioInf2305
-modules/nf-core/simpleaf/index/** @fmalmeida @maxulysse @Khajidu @apeltzer @pinin4fjords
-modules/nf-core/simpleaf/quant/** @fmalmeida @maxulysse @Khajidu @apeltzer @pinin4fjords
-modules/nf-core/sistr/** @rpetit3
-modules/nf-core/slimfastq/** @Midnighter
-modules/nf-core/smncopynumbercaller/** @peterpru
-modules/nf-core/smoothxg/** @heuermh, @subwaystation
-modules/nf-core/smoove/call/** @scorreard @nvnieuwk
-modules/nf-core/snakemake/** @adamrtalbot
-modules/nf-core/snapaligner/align/** @matthdsm
-modules/nf-core/snapaligner/index/** @matthdsm
-modules/nf-core/sniffles/** @christopher-hakkaart @yuukiiwa
-modules/nf-core/snippy/core/** @rpetit3
-modules/nf-core/snippy/run/** @rpetit3
-modules/nf-core/snpdists/** @abhi18av
-modules/nf-core/snpeff/download/** @maxulysse
-modules/nf-core/snpeff/snpeff/** @maxulysse
-modules/nf-core/snpsift/annotate/** @LlaneroHiboreo
-modules/nf-core/snpsift/dbnsfp/** @LlaneroHiboreo
-modules/nf-core/snpsift/split/** @SusiJo @jonasscheid
-modules/nf-core/snpsites/** @avantonder
-modules/nf-core/somalier/ancestry/** @atrigila
-modules/nf-core/somalier/extract/** @ashotmarg @nvnieuwk
-modules/nf-core/somalier/relate/** @ashotmarg @nvnieuwk
-modules/nf-core/sortmerna/** @drpatelh @mashehu
-modules/nf-core/sourmash/compare/** @taylorreiter
-modules/nf-core/sourmash/gather/** @vmikk @taylorreiter
-modules/nf-core/sourmash/index/** @emnilsson
-modules/nf-core/sourmash/sketch/** @Midnighter
-modules/nf-core/sourmash/taxannotate/** @vmikk @taylorreiter
-modules/nf-core/spaceranger/count/** @grst
-modules/nf-core/spaceranger/mkgtf/** @grst
-modules/nf-core/spaceranger/mkref/** @grst
-modules/nf-core/spades/** @JoseEspinosa @drpatelh @d4straub
-modules/nf-core/spatyper/** @rpetit3
-modules/nf-core/spring/compress/** @xec-cm
-modules/nf-core/spring/decompress/** @xec-cm
-modules/nf-core/sratools/fasterqdump/** @Midnighter
-modules/nf-core/sratools/prefetch/** @Midnighter
-modules/nf-core/srst2/srst2/** @jvhagey
-modules/nf-core/ssuissero/** @rpetit3
-modules/nf-core/stadeniolib/scramble/** @matthdsm
-modules/nf-core/staphopiasccmec/** @rpetit3
-modules/nf-core/star/align/** @kevinmenden @drpatelh @praveenraj2018
-modules/nf-core/star/genomegenerate/** @kevinmenden @drpatelh
-modules/nf-core/star/starsolo/** @kevinmenden @ggabernet @grst @fmalmeida @rhreynolds @apeltzer @vivian-chen16 @maxulysse @joaodemeirelles
-modules/nf-core/stecfinder/** @rpetit3
-modules/nf-core/stitch/** @saulpierotti
-modules/nf-core/stranger/** @ljmesi
-modules/nf-core/strelka/germline/** @arontommi
-modules/nf-core/strelka/somatic/** @drpatelh
-modules/nf-core/stringtie/merge/** @yuukiiwa
-modules/nf-core/stringtie/stringtie/** @drpatelh
-modules/nf-core/subread/featurecounts/** @ntoda03
-modules/nf-core/survivor/filter/** @LlaneroHiboreo
-modules/nf-core/survivor/merge/** @nvnieuwk
-modules/nf-core/survivor/simsv/** @nvnieuwk
-modules/nf-core/svaba/** @kubranarci
-modules/nf-core/svdb/merge/** @ramprasadn
-modules/nf-core/svdb/query/** @ramprasadn
-modules/nf-core/svtk/baftest/** @nvnieuwk
-modules/nf-core/svtk/countsvtypes/** @nvnieuwk
-modules/nf-core/svtk/rdtest2vcf/** @nvnieuwk
-modules/nf-core/svtk/standardize/** @nvnieuwk
-modules/nf-core/svtk/vcf2bed/** @nvnieuwk
-modules/nf-core/svtyper/svtyper/** @kubranarci
-modules/nf-core/tabix/bgzip/** @joseespinosa @drpatelh @maxulysse @nvnieuwk
-modules/nf-core/tabix/bgziptabix/** @maxulysse @DLBPointon
-modules/nf-core/tabix/tabix/** @joseespinosa @drpatelh @maxulysse
-modules/nf-core/tailfindr/** @lucacozzuto
-modules/nf-core/taxpasta/merge/** @sofstam @jfy133
-modules/nf-core/taxpasta/standardise/** @Midnighter
-modules/nf-core/tbprofiler/profile/** @rpetit3
-modules/nf-core/tcoffee/align/** @luisas
-modules/nf-core/tiara/tiara/** @prototaxites
-modules/nf-core/tiddit/cov/** @projectoriented @ramprasadn
-modules/nf-core/tiddit/sv/** @maxulysse
-modules/nf-core/topas/gencons/** @aidaanva
-modules/nf-core/transdecoder/longorf/** @Danilo2771
-modules/nf-core/transdecoder/predict/** @Danilo2771
-modules/nf-core/trimgalore/** @drpatelh @FelixKrueger
-modules/nf-core/trimmomatic/** @alyssa-ab
-modules/nf-core/trinity/** @timslittle
-modules/nf-core/truvari/bench/** @nvnieuwk
-modules/nf-core/ucsc/bedclip/** @drpatelh
-modules/nf-core/ucsc/bedgraphtobigwig/** @drpatelh
-modules/nf-core/ucsc/bedtobigbed/** @drpatelh
-modules/nf-core/ucsc/bigwigaverageoverbed/** @jianhong
-modules/nf-core/ucsc/gtftogenepred/** @BarryDigby @anoronh4
-modules/nf-core/ucsc/liftover/** @nebfield
-modules/nf-core/ucsc/wigtobigwig/** @jianhong @projectoriented
-modules/nf-core/ultra/align/** @sguizard
-modules/nf-core/ultra/index/** @sguizard
-modules/nf-core/ultra/pipeline/** @sguizard @lassefolkersen @ksahlin
-modules/nf-core/ultraplex/** @CharlotteAnne @oscarwilkins @chris-cheshire @marc-jones @iraiosub @samirelanduk
-modules/nf-core/umicollapse/** @CharlotteAnne @chris-cheshire
-modules/nf-core/umitools/dedup/** @drpatelh @grst @klkeys
-modules/nf-core/umitools/extract/** @drpatelh @grst
-modules/nf-core/umitools/group/** @Joon-Klaps
-modules/nf-core/unicycler/** @JoseEspinosa @drpatelh @d4straub
-modules/nf-core/universc/** @kbattenb @tomkellygenetics
-modules/nf-core/untarfiles/** @joseespinosa @drpatelh @matthdsm @jfy133 @pinin4fjords
-modules/nf-core/untar/** @joseespinosa @drpatelh @matthdsm @jfy133
-modules/nf-core/unzipfiles/** @jfy133 @pinin4fjords
-modules/nf-core/unzip/** @jfy133
-modules/nf-core/upd/** @hrydbeck
-modules/nf-core/vardictjava/** @nvnieuwk
-modules/nf-core/variantbam/** @bjohnnyd
-modules/nf-core/varlociraptor/callvariants/** @FriederikeHanssen
-modules/nf-core/varlociraptor/estimatealignmentproperties/** @FriederikeHanssen
-modules/nf-core/varlociraptor/preprocess/** @FriederikeHanssen
-modules/nf-core/vcf2db/** @nvnieuwk
-modules/nf-core/vcf2maf/** @adamrtalbot
-modules/nf-core/vcfanno/** @projectoriented @matthdsm
-modules/nf-core/vcflib/vcfbreakmulti/** @lucpen
-modules/nf-core/vcflib/vcffilter/** @zachary-foster
-modules/nf-core/vcflib/vcfuniq/** @drpatelh
-modules/nf-core/vcftools/** @Mark-S-Hill
-modules/nf-core/verifybamid/verifybamid2/** @manifestoso
-modules/nf-core/verifybamid/verifybamid/** @manifestoso
-modules/nf-core/vg/construct/** @nvnieuwk
-modules/nf-core/vg/deconstruct/** @heuermh, @subwaystation
-modules/nf-core/vg/index/** @nvnieuwk
-modules/nf-core/vrhyme/extractunbinned/** @CarsonJM
-modules/nf-core/vrhyme/linkbins/** @CarsonJM
-modules/nf-core/vrhyme/vrhyme/** @CarsonJM
-modules/nf-core/vsearch/cluster/** @mirpedrol
-modules/nf-core/vsearch/sintax/** @jtangrot
-modules/nf-core/vsearch/sort/** @mirpedrol
-modules/nf-core/vsearch/usearchglobal/** @jtangrot
-modules/nf-core/vt/decompose/** @nvnieuwk
-modules/nf-core/vt/normalize/** @nvnieuwk
-modules/nf-core/wfmash/** @subwaystation
-modules/nf-core/wgsim/** @priyanka-surana
-modules/nf-core/whamg/** @nvnieuwk
-modules/nf-core/windowmasker/convert/** @alxndrdiaz
-modules/nf-core/windowmasker/mkcounts/** @DLBPointon
-modules/nf-core/windowmasker/ustat/** @DLBPointon
-modules/nf-core/wisecondorx/convert/** @nvnieuwk
-modules/nf-core/wisecondorx/gender/** @nvnieuwk
-modules/nf-core/wisecondorx/newref/** @nvnieuwk
-modules/nf-core/wisecondorx/predict/** @nvnieuwk
-modules/nf-core/yahs/** @ksenia-krasheninnikova
-modules/nf-core/yara/index/** @apeltzer
-modules/nf-core/yara/mapper/** @apeltzer
-modules/nf-core/zip/** @jfy133 @pinin4fjords
-subworkflows/nf-core/bam_cnv_wisecondorx/** @nvnieuwk
-subworkflows/nf-core/bam_create_som_pon_gatk/** @GCJMackenzie
-subworkflows/nf-core/bam_dedup_stats_samtools_umitools/** @drpatelh @KamilMaliszArdigen
-subworkflows/nf-core/bam_docounts_contamination_angsd/** @scarlhoff
-subworkflows/nf-core/bam_markduplicates_picard/** @dmarron @drpatelh
-subworkflows/nf-core/bam_markduplicates_samtools/** @priyanka-surana
-subworkflows/nf-core/bam_ngscheckmate/** @SPPearce
-subworkflows/nf-core/bam_qc_picard/** @matthdsm
-subworkflows/nf-core/bam_rseqc/** @drpatelh @kevinmenden
-subworkflows/nf-core/bam_sort_stats_samtools/** @drpatelh
-subworkflows/nf-core/bam_split_by_region/** @TCLamnidis
-subworkflows/nf-core/bam_stats_samtools/** @drpatelh
-subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/** @GCJMackenzie
-subworkflows/nf-core/bam_tumor_only_somatic_variant_calling_gatk/** @GCJMackenzie
-subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/** @priyanka-surana @FriederikeHanssen @ramprasadn
-subworkflows/nf-core/bam_variant_demix_boot_freyja/** @Joon-Klaps
-subworkflows/nf-core/bcl_demultiplex/** @matthdsm
-subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/** @drpatelh @KamilMaliszArdigen
-subworkflows/nf-core/bed_scatter_bedtools/** @nvnieuwk
-subworkflows/nf-core/fasta_binning_concoct/** @jfy133
-subworkflows/nf-core/fasta_clean_fcs/** @scorreard
-subworkflows/nf-core/fasta_index_dna/** @matthdsm @ramprasadn
-subworkflows/nf-core/fasta_newick_epang_gappa/** @erikrikarddaniel
-subworkflows/nf-core/fastq_align_bamcmp_bwa/** @sppearce
-subworkflows/nf-core/fastq_align_bowtie2/** @drpatelh
-subworkflows/nf-core/fastq_align_bwaaln/** @jfy133
-subworkflows/nf-core/fastq_align_bwa/** @JoseEspinosa
-subworkflows/nf-core/fastq_align_chromap/** @JoseEspinosa
-subworkflows/nf-core/fastq_align_dna/** @matthdsm
-subworkflows/nf-core/fastq_align_hisat2/** @priyanka-surana
-subworkflows/nf-core/fastq_align_star/** @JoseEspinosa
-subworkflows/nf-core/fastq_contam_seqtk_kraken/** @apeltzer
-subworkflows/nf-core/fastq_create_umi_consensus_fgbio/** @lescai
-subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/** @Midnighter @drpatelh
-subworkflows/nf-core/fastq_fastqc_umitools_fastp/** @robsyme
-subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/** @drpatelh @KamilMaliszArdigen
-subworkflows/nf-core/fastq_ngscheckmate/** @SPPearce
-subworkflows/nf-core/fastq_subsample_fq_salmon/** @robsyme @drpatelh
-subworkflows/nf-core/fastq_trim_fastp_fastqc/** @Joon-Klaps
-subworkflows/nf-core/homer/groseq/** @edmundmiller
-subworkflows/nf-core/initialise/** @adamrtalbot
-subworkflows/nf-core/multiple_impute_glimpse2/** @LouisLeNezet
-subworkflows/nf-core/utils_nextflow_pipeline/** @adamrtalbot @drpatelh
-subworkflows/nf-core/utils_nf_core_pipeline/** @adamrtalbot @drpatelh
-subworkflows/nf-core/utils_nf_validataion_pipeline/** @adamrtalbot @drpatelh
-subworkflows/nf-core/vcf_annotate_ensemblvep/** @maxulysse @matthdsm @nvnieuwk
-subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/** @maxulysse @matthdsm @nvnieuwk
-subworkflows/nf-core/vcf_annotate_snpeff/** @maxulysse
-subworkflows/nf-core/vcf_extract_relate_somalier/** @nvnieuwk
-subworkflows/nf-core/vcf_gather_bcftools/** @nvnieuwk
-subworkflows/nf-core/vcf_impute_glimpse/** @LouisLeNezet
-subworkflows/nf-core/vcf_phase_shapeit5/** @LouisLeNezet
+modules/nf-core/preseq/ccurve/** @edmundmiller
+modules/nf-core/preseq/lcextrap/** @edmundmiller
+subworkflows/nf-core/homer/** @edmundmiller
diff --git a/modules/nf-core/genmod/annotate/environment.yml b/modules/nf-core/genmod/annotate/environment.yml
index 1eca76fad2c..bbc3fd973a9 100644
--- a/modules/nf-core/genmod/annotate/environment.yml
+++ b/modules/nf-core/genmod/annotate/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.8.2
+  - bioconda::genmod=3.8.3
diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf
index eb161187687..033caa9ae93 100644
--- a/modules/nf-core/genmod/annotate/main.nf
+++ b/modules/nf-core/genmod/annotate/main.nf
@@ -4,8 +4,8 @@ process GENMOD_ANNOTATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0':
+        'biocontainers/genmod:3.8.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
diff --git a/modules/nf-core/genmod/compound/environment.yml b/modules/nf-core/genmod/compound/environment.yml
index 1eca76fad2c..bbc3fd973a9 100644
--- a/modules/nf-core/genmod/compound/environment.yml
+++ b/modules/nf-core/genmod/compound/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.8.2
+  - bioconda::genmod=3.8.3
diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf
index 1731b722224..4831da855fa 100644
--- a/modules/nf-core/genmod/compound/main.nf
+++ b/modules/nf-core/genmod/compound/main.nf
@@ -4,8 +4,8 @@ process GENMOD_COMPOUND {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0':
+        'biocontainers/genmod:3.8.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
diff --git a/modules/nf-core/genmod/models/environment.yml b/modules/nf-core/genmod/models/environment.yml
index 1eca76fad2c..bbc3fd973a9 100644
--- a/modules/nf-core/genmod/models/environment.yml
+++ b/modules/nf-core/genmod/models/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.8.2
+  - bioconda::genmod=3.8.3
diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf
index 0504574a194..90c1fd48233 100644
--- a/modules/nf-core/genmod/models/main.nf
+++ b/modules/nf-core/genmod/models/main.nf
@@ -4,8 +4,8 @@ process GENMOD_MODELS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0':
+        'biocontainers/genmod:3.8.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
diff --git a/modules/nf-core/genmod/score/environment.yml b/modules/nf-core/genmod/score/environment.yml
index 1eca76fad2c..bbc3fd973a9 100644
--- a/modules/nf-core/genmod/score/environment.yml
+++ b/modules/nf-core/genmod/score/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.8.2
+  - bioconda::genmod=3.8.3
diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf
index 15be5f744b3..522e05b6581 100644
--- a/modules/nf-core/genmod/score/main.nf
+++ b/modules/nf-core/genmod/score/main.nf
@@ -4,8 +4,8 @@ process GENMOD_SCORE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0':
+        'biocontainers/genmod:3.8.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
diff --git a/modules/nf-core/longphase/haplotag/main.nf b/modules/nf-core/longphase/haplotag/main.nf
index 701af31fe54..86ba0592556 100644
--- a/modules/nf-core/longphase/haplotag/main.nf
+++ b/modules/nf-core/longphase/haplotag/main.nf
@@ -24,8 +24,8 @@ process LONGPHASE_HAPLOTAG {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def sv_file = params.svs ? "--sv-file ${svs}" : ""
-    def mod_file = params.mods ? "--mod-file ${mods}" : ""
+    def sv_file = svs ? "--sv-file ${svs}" : ""
+    def mod_file = mods ? "--mod-file ${mods}" : ""
 
     """
     longphase \\
diff --git a/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap b/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap
index 225a4f7ed85..3cf35dc32ff 100644
--- a/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap
+++ b/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap
@@ -119,15 +119,15 @@
                 "@RG\tID:test\tSM:test",
                 "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -y -x map-ont --secondary=no -R @RG\\tID:test\\tSM:test -t 30 -a genome.mmi test.bam_other.fastq.gz",
                 "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.19.2\tCL:samtools sort -@ 29 -o test.bam_other.fastq.gz.bam --write-index",
-                "@PG\tID:longphase\tPN:longphase\tPP:samtools\tVN:1.7.3\tCL:longphase haplotag --threads 2 -o test --reference genome.fasta --snp-file test.genome.vcf.gz --bam test.sorted.bam "
+                "@PG\tID:longphase\tPN:longphase\tPP:samtools\tVN:1.7.3\tCL:longphase haplotag --threads 2 -o test --reference genome.fasta --snp-file test.genome.vcf.gz --bam test.sorted.bam --sv-file NA24385_sv.vcf.gz "
             ],
             "721264eb2824a3146b331f2532d10180"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-25T09:13:39.901419316"
+        "timestamp": "2024-10-04T13:39:33.50395694"
     },
     "[ bam, bai, snps, [], [] ], fasta, fai - log & cram": {
         "content": [
diff --git a/modules/nf-core/longphase/phase/main.nf b/modules/nf-core/longphase/phase/main.nf
index ad29d997288..f121f4b6dd6 100644
--- a/modules/nf-core/longphase/phase/main.nf
+++ b/modules/nf-core/longphase/phase/main.nf
@@ -24,8 +24,8 @@ process LONGPHASE_PHASE {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def sv_file = params.svs ? "--sv-file ${svs}" : ""
-    def mod_file = params.mods ? "--mod-file ${mods}" : ""
+    def sv_file = svs ? "--sv-file ${svs}" : ""
+    def mod_file = mods ? "--mod-file ${mods}" : ""
 
     def bamList = []
     for (file in bam) {
diff --git a/modules/nf-core/longphase/phase/tests/main.nf.test.snap b/modules/nf-core/longphase/phase/tests/main.nf.test.snap
index 02e2bb1731f..8a38c1caa5c 100644
--- a/modules/nf-core/longphase/phase/tests/main.nf.test.snap
+++ b/modules/nf-core/longphase/phase/tests/main.nf.test.snap
@@ -40,7 +40,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,fd2d21056b2de4722f12d5e883d9cb0a"
+                        "test.vcf.gz:md5,b0a3effd6e076edbe7e2f1f7cfff547c"
                     ]
                 ],
                 "1": [
@@ -51,7 +51,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,fd2d21056b2de4722f12d5e883d9cb0a"
+                        "test.vcf.gz:md5,b0a3effd6e076edbe7e2f1f7cfff547c"
                     ]
                 ],
                 "versions": [
@@ -60,10 +60,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T12:14:39.961315592"
+        "timestamp": "2024-10-04T13:37:16.921910004"
     },
     "[ bam x2, bai x2, snps, svs, [] ], fasta, fai": {
         "content": [
@@ -73,7 +73,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,3ced25dc8c1ec0a7c64481c8a163d687"
+                        "test.vcf.gz:md5,04905b6042998e592c9f3b887ae9e09c"
                     ]
                 ],
                 "1": [
@@ -84,7 +84,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,3ced25dc8c1ec0a7c64481c8a163d687"
+                        "test.vcf.gz:md5,04905b6042998e592c9f3b887ae9e09c"
                     ]
                 ],
                 "versions": [
@@ -93,10 +93,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T12:15:07.970597495"
+        "timestamp": "2024-10-04T13:37:23.41768963"
     },
     "[ bam, bai, snps, [], [] ], fasta, fai - stub": {
         "content": [
diff --git a/modules/nf-core/motus/preplong/environment.yml b/modules/nf-core/motus/preplong/environment.yml
new file mode 100644
index 00000000000..b8ef520eaa2
--- /dev/null
+++ b/modules/nf-core/motus/preplong/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::motus=3.1.0
diff --git a/modules/nf-core/motus/preplong/main.nf b/modules/nf-core/motus/preplong/main.nf
new file mode 100644
index 00000000000..3fffc149648
--- /dev/null
+++ b/modules/nf-core/motus/preplong/main.nf
@@ -0,0 +1,53 @@
+process MOTUS_PREPLONG {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/motus:3.1.0--pyhdfd78af_0':
+        'biocontainers/motus:3.1.0--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path db
+
+    output:
+    tuple val(meta), path("*.gz"), emit: out
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def refdb = db ? "-db ${db}" : ""
+
+    """
+    motus \\
+        prep_long \\
+        $args \\
+        -i $reads \\
+        $refdb \\
+        -t $task.cpus \\
+        -o ${prefix}.gz \\
+        2> >(tee ${prefix}.log >&2)
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        motus: \$(motus --version 2>&1 | sed 's/.* \\([0-9]*\\.[0-9]*\\.[0-9]*\\) .*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo '' | gzip > ${prefix}.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        motus: \$(motus --version 2>&1 | sed 's/.* \\([0-9]*\\.[0-9]*\\.[0-9]*\\) .*/\\1/')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
new file mode 100644
index 00000000000..6ef63949a04
--- /dev/null
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -0,0 +1,52 @@
+name: "motus_preplong"
+description: Taxonomic meta-omics profiling using universal marker genes
+keywords:
+  - classify
+  - metagenomics
+  - fastq
+  - taxonomic profiling
+tools:
+  - "motus":
+      description: "Marker gene-based operational taxonomic unit (mOTU) profiling"
+      homepage: "https://motu-tool.org/"
+      documentation: "https://github.com/motu-tool/mOTUs/wiki"
+      tool_dev_url: "https://github.com/motu-tool/mOTUs"
+      doi: "10.1186/s40168-022-01410-z"
+      licence: ["GPL v3"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - reads:
+        type: file
+        description: Long read file to convert, can be fasta(.gz) or fastq(.gz)
+        pattern: "*.{gz}"
+  - - db:
+        type: directory
+        description: |
+          mOTUs database downloaded by `motus downloadDB`
+          pattern: "db_mOTU/"
+output:
+  - out:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.gz":
+          type: file
+          description: converted file (gzipped), ready to be used by motus profile
+          pattern: "*.gz"
+  - versions:
+      - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@sofstam"
+maintainers:
+  - "@sofstam"
diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test b/modules/nf-core/motus/preplong/tests/main.nf.test
new file mode 100644
index 00000000000..5ad8e7487f1
--- /dev/null
+++ b/modules/nf-core/motus/preplong/tests/main.nf.test
@@ -0,0 +1,75 @@
+nextflow_process {
+
+    name "Test Process MOTUS_PREPLONG"
+    script "../main.nf"
+    process "MOTUS_PREPLONG"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "motus"
+    tag "motus/downloaddb"
+    tag "motus/preplong"
+
+    setup {
+        run("MOTUS_DOWNLOADDB") {
+            script "modules/nf-core/motus/downloaddb/main.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py')
+                ])
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
+                ]
+                input[1] =  MOTUS_DOWNLOADDB.out.db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
+                ]
+                input[1] =  MOTUS_DOWNLOADDB.out.db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+
+    }
+
+}
diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test.snap b/modules/nf-core/motus/preplong/tests/main.nf.test.snap
new file mode 100644
index 00000000000..5ed72ec8a9a
--- /dev/null
+++ b/modules/nf-core/motus/preplong/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb"
+                ],
+                "out": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-09-06T16:29:18.602046"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gz:md5,37be4a7321bcb2fdae60affb21a1737c"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb"
+                ],
+                "out": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gz:md5,37be4a7321bcb2fdae60affb21a1737c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-09-06T15:55:48.439664"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/motus/preplong/tests/tags.yml b/modules/nf-core/motus/preplong/tests/tags.yml
new file mode 100644
index 00000000000..bdaae3b2032
--- /dev/null
+++ b/modules/nf-core/motus/preplong/tests/tags.yml
@@ -0,0 +1,2 @@
+motus/preplong:
+  - "modules/nf-core/motus/preplong/**"
diff --git a/modules/nf-core/severus/tests/main.nf.test b/modules/nf-core/severus/tests/main.nf.test
index 1b85a109f04..ab700a4c12c 100644
--- a/modules/nf-core/severus/tests/main.nf.test
+++ b/modules/nf-core/severus/tests/main.nf.test
@@ -7,7 +7,6 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "severus"
-    tag "deepvariant"
 
     test("homo_sapiens - [ bam, bai, [], [], [] ], [[],[]]") {
 
@@ -206,4 +205,4 @@ nextflow_process {
 
     }
 
-}
\ No newline at end of file
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
index 5784a33f2f5..c50b1fb5323 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -169,7 +169,7 @@ nextflow_workflow {
             params {
                 monochrome_logs = true
                 test_data       = ''
-                outdir          = 1
+                outdir          = false
             }
             workflow {
                 """