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Restructure nf-core/modules repo #2141

Merged

drpatelh merged 9 commits into nf-core:master from drpatelh:boom

Oct 4, 2022

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0 modules/abacas/main.nf → modules/nf-core/abacas/main.nf

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0 modules/abacas/meta.yml → modules/nf-core/abacas/meta.yml

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0 modules/abricate/run/main.nf → modules/nf-core/abricate/run/main.nf

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0 modules/abricate/run/meta.yml → modules/nf-core/abricate/run/meta.yml

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0 modules/abricate/summary/main.nf → modules/nf-core/abricate/summary/main.nf

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0 modules/abricate/summary/meta.yml → modules/nf-core/abricate/summary/meta.yml

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0 modules/adapterremoval/main.nf → modules/nf-core/adapterremoval/main.nf

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0 modules/adapterremoval/meta.yml → modules/nf-core/adapterremoval/meta.yml

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0 modules/adapterremovalfixprefix/main.nf → ...s/nf-core/adapterremovalfixprefix/main.nf

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0 modules/adapterremovalfixprefix/meta.yml → .../nf-core/adapterremovalfixprefix/meta.yml

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0 modules/agrvate/main.nf → modules/nf-core/agrvate/main.nf

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0 modules/agrvate/meta.yml → modules/nf-core/agrvate/meta.yml

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0 modules/allelecounter/main.nf → modules/nf-core/allelecounter/main.nf

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0 modules/allelecounter/meta.yml → modules/nf-core/allelecounter/meta.yml

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0 modules/ampir/main.nf → modules/nf-core/ampir/main.nf

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0 modules/ampir/meta.yml → modules/nf-core/ampir/meta.yml

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0 modules/amplify/predict/main.nf → modules/nf-core/amplify/predict/main.nf

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0 modules/amplify/predict/meta.yml → modules/nf-core/amplify/predict/meta.yml

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0 modules/amps/main.nf → modules/nf-core/amps/main.nf

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0 modules/amps/meta.yml → modules/nf-core/amps/meta.yml

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0 modules/amrfinderplus/run/main.nf → modules/nf-core/amrfinderplus/run/main.nf

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0 modules/amrfinderplus/run/meta.yml → modules/nf-core/amrfinderplus/run/meta.yml

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0 modules/amrfinderplus/update/main.nf → modules/nf-core/amrfinderplus/update/main.nf

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0 modules/amrfinderplus/update/meta.yml → ...les/nf-core/amrfinderplus/update/meta.yml

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0 modules/angsd/docounts/main.nf → modules/nf-core/angsd/docounts/main.nf

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0 modules/angsd/docounts/meta.yml → modules/nf-core/angsd/docounts/meta.yml

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0 modules/antismash/antismashlite/main.nf → ...s/nf-core/antismash/antismashlite/main.nf

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0 modules/antismash/antismashlite/meta.yml → .../nf-core/antismash/antismashlite/meta.yml

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0 ...sh/antismashlitedownloaddatabases/main.nf → ...sh/antismashlitedownloaddatabases/main.nf

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0 ...h/antismashlitedownloaddatabases/meta.yml → ...h/antismashlitedownloaddatabases/meta.yml

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0 modules/ariba/getref/main.nf → modules/nf-core/ariba/getref/main.nf

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0 modules/ariba/getref/meta.yml → modules/nf-core/ariba/getref/meta.yml

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0 modules/ariba/run/main.nf → modules/nf-core/ariba/run/main.nf

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0 modules/ariba/run/meta.yml → modules/nf-core/ariba/run/meta.yml

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0 modules/arriba/main.nf → modules/nf-core/arriba/main.nf

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0 modules/arriba/meta.yml → modules/nf-core/arriba/meta.yml

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0 modules/artic/guppyplex/main.nf → modules/nf-core/artic/guppyplex/main.nf

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0 modules/artic/guppyplex/meta.yml → modules/nf-core/artic/guppyplex/meta.yml

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0 modules/artic/minion/main.nf → modules/nf-core/artic/minion/main.nf

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0 modules/artic/minion/meta.yml → modules/nf-core/artic/minion/meta.yml

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0 modules/ascat/main.nf → modules/nf-core/ascat/main.nf

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0 modules/ascat/meta.yml → modules/nf-core/ascat/meta.yml

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0 modules/assemblyscan/main.nf → modules/nf-core/assemblyscan/main.nf

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0 modules/assemblyscan/meta.yml → modules/nf-core/assemblyscan/meta.yml

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0 modules/ataqv/ataqv/main.nf → modules/nf-core/ataqv/ataqv/main.nf

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0 modules/ataqv/ataqv/meta.yml → modules/nf-core/ataqv/ataqv/meta.yml

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0 modules/ataqv/mkarv/main.nf → modules/nf-core/ataqv/mkarv/main.nf

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0 modules/ataqv/mkarv/meta.yml → modules/nf-core/ataqv/mkarv/meta.yml

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0 modules/atlas/call/main.nf → modules/nf-core/atlas/call/main.nf

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0 modules/atlas/call/meta.yml → modules/nf-core/atlas/call/meta.yml

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0 modules/atlas/pmd/main.nf → modules/nf-core/atlas/pmd/main.nf

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0 modules/atlas/pmd/meta.yml → modules/nf-core/atlas/pmd/meta.yml

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0 modules/atlas/recal/main.nf → modules/nf-core/atlas/recal/main.nf

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0 modules/atlas/recal/meta.yml → modules/nf-core/atlas/recal/meta.yml

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0 modules/atlas/splitmerge/main.nf → modules/nf-core/atlas/splitmerge/main.nf

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0 modules/atlas/splitmerge/meta.yml → modules/nf-core/atlas/splitmerge/meta.yml

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0 modules/bakta/main.nf → modules/nf-core/bakta/main.nf

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0 modules/bakta/meta.yml → modules/nf-core/bakta/meta.yml

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0 modules/bamaligncleaner/main.nf → modules/nf-core/bamaligncleaner/main.nf

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0 modules/bamaligncleaner/meta.yml → modules/nf-core/bamaligncleaner/meta.yml

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0 modules/bamcmp/main.nf → modules/nf-core/bamcmp/main.nf

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0 modules/bamcmp/meta.yml → modules/nf-core/bamcmp/meta.yml

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0 modules/bamtools/convert/main.nf → modules/nf-core/bamtools/convert/main.nf

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0 modules/bamtools/convert/meta.yml → modules/nf-core/bamtools/convert/meta.yml

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0 modules/bamtools/split/main.nf → modules/nf-core/bamtools/split/main.nf

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0 modules/bamtools/split/meta.yml → modules/nf-core/bamtools/split/meta.yml

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0 modules/bamtools/stats/main.nf → modules/nf-core/bamtools/stats/main.nf

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0 modules/bamtools/stats/meta.yml → modules/nf-core/bamtools/stats/meta.yml

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0 modules/bamutil/trimbam/main.nf → modules/nf-core/bamutil/trimbam/main.nf

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0 modules/bamutil/trimbam/meta.yml → modules/nf-core/bamutil/trimbam/meta.yml

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0 modules/bandage/image/main.nf → modules/nf-core/bandage/image/main.nf

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0 modules/bandage/image/meta.yml → modules/nf-core/bandage/image/meta.yml

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0 modules/bases2fastq/main.nf → modules/nf-core/bases2fastq/main.nf

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0 modules/bases2fastq/meta.yml → modules/nf-core/bases2fastq/meta.yml

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0 modules/bbmap/align/main.nf → modules/nf-core/bbmap/align/main.nf

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0 modules/bbmap/align/meta.yml → modules/nf-core/bbmap/align/meta.yml

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0 modules/bbmap/bbduk/main.nf → modules/nf-core/bbmap/bbduk/main.nf

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0 modules/bbmap/bbduk/meta.yml → modules/nf-core/bbmap/bbduk/meta.yml

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0 modules/bbmap/bbsplit/main.nf → modules/nf-core/bbmap/bbsplit/main.nf

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0 modules/bbmap/bbsplit/meta.yml → modules/nf-core/bbmap/bbsplit/meta.yml

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0 modules/bbmap/clumpify/main.nf → modules/nf-core/bbmap/clumpify/main.nf

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0 modules/bbmap/clumpify/meta.yml → modules/nf-core/bbmap/clumpify/meta.yml

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0 modules/bbmap/index/main.nf → modules/nf-core/bbmap/index/main.nf

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0 modules/bbmap/index/meta.yml → modules/nf-core/bbmap/index/meta.yml

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0 modules/bbmap/pileup/main.nf → modules/nf-core/bbmap/pileup/main.nf

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0 modules/bbmap/pileup/meta.yml → modules/nf-core/bbmap/pileup/meta.yml

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0 modules/bcftools/annotate/main.nf → modules/nf-core/bcftools/annotate/main.nf

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0 modules/bcftools/annotate/meta.yml → modules/nf-core/bcftools/annotate/meta.yml

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0 modules/bcftools/concat/main.nf → modules/nf-core/bcftools/concat/main.nf

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0 modules/bcftools/concat/meta.yml → modules/nf-core/bcftools/concat/meta.yml

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0 modules/bcftools/consensus/main.nf → modules/nf-core/bcftools/consensus/main.nf

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0 modules/bcftools/consensus/meta.yml → modules/nf-core/bcftools/consensus/meta.yml

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0 modules/bcftools/convert/main.nf → modules/nf-core/bcftools/convert/main.nf

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0 modules/bcftools/convert/meta.yml → modules/nf-core/bcftools/convert/meta.yml

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0 modules/bcftools/filter/main.nf → modules/nf-core/bcftools/filter/main.nf

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0 modules/bcftools/filter/meta.yml → modules/nf-core/bcftools/filter/meta.yml

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0 modules/bcftools/index/main.nf → modules/nf-core/bcftools/index/main.nf

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0 modules/bcftools/index/meta.yml → modules/nf-core/bcftools/index/meta.yml

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0 modules/bcftools/isec/main.nf → modules/nf-core/bcftools/isec/main.nf

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0 modules/bcftools/isec/meta.yml → modules/nf-core/bcftools/isec/meta.yml

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0 modules/bcftools/merge/main.nf → modules/nf-core/bcftools/merge/main.nf

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0 modules/bcftools/merge/meta.yml → modules/nf-core/bcftools/merge/meta.yml

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0 modules/bcftools/mpileup/main.nf → modules/nf-core/bcftools/mpileup/main.nf

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0 modules/bcftools/mpileup/meta.yml → modules/nf-core/bcftools/mpileup/meta.yml

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0 modules/bcftools/norm/main.nf → modules/nf-core/bcftools/norm/main.nf

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0 modules/bcftools/norm/meta.yml → modules/nf-core/bcftools/norm/meta.yml

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0 modules/bcftools/query/main.nf → modules/nf-core/bcftools/query/main.nf

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0 modules/bcftools/query/meta.yml → modules/nf-core/bcftools/query/meta.yml

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0 modules/bcftools/reheader/main.nf → modules/nf-core/bcftools/reheader/main.nf

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0 modules/bcftools/reheader/meta.yml → modules/nf-core/bcftools/reheader/meta.yml

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0 modules/bcftools/roh/main.nf → modules/nf-core/bcftools/roh/main.nf

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0 modules/bcftools/roh/meta.yml → modules/nf-core/bcftools/roh/meta.yml

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0 modules/bcftools/sort/main.nf → modules/nf-core/bcftools/sort/main.nf

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0 modules/bcftools/sort/meta.yml → modules/nf-core/bcftools/sort/meta.yml

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0 modules/bcftools/stats/main.nf → modules/nf-core/bcftools/stats/main.nf

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0 modules/bcftools/stats/meta.yml → modules/nf-core/bcftools/stats/meta.yml

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0 modules/bcftools/view/main.nf → modules/nf-core/bcftools/view/main.nf

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0 modules/bcftools/view/meta.yml → modules/nf-core/bcftools/view/meta.yml

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0 modules/bcl2fastq/.gitignore → modules/nf-core/bcl2fastq/.gitignore

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0 modules/bcl2fastq/Dockerfile → modules/nf-core/bcl2fastq/Dockerfile

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0 modules/bcl2fastq/LICENSE → modules/nf-core/bcl2fastq/LICENSE

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0 modules/bcl2fastq/README.md → modules/nf-core/bcl2fastq/README.md

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0 modules/bcl2fastq/main.nf → modules/nf-core/bcl2fastq/main.nf

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0 modules/bcl2fastq/meta.yml → modules/nf-core/bcl2fastq/meta.yml

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0 modules/bclconvert/.gitignore → modules/nf-core/bclconvert/.gitignore

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0 modules/bclconvert/Dockerfile → modules/nf-core/bclconvert/Dockerfile

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0 modules/bclconvert/LICENSE → modules/nf-core/bclconvert/LICENSE

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0 modules/bclconvert/README.md → modules/nf-core/bclconvert/README.md

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0 modules/bclconvert/main.nf → modules/nf-core/bclconvert/main.nf

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0 modules/bclconvert/meta.yml → modules/nf-core/bclconvert/meta.yml

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0 modules/bedtools/bamtobed/main.nf → modules/nf-core/bedtools/bamtobed/main.nf

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0 modules/bedtools/bamtobed/meta.yml → modules/nf-core/bedtools/bamtobed/meta.yml

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0 modules/bedtools/complement/main.nf → modules/nf-core/bedtools/complement/main.nf

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0 modules/bedtools/complement/meta.yml → modules/nf-core/bedtools/complement/meta.yml

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0 modules/bedtools/genomecov/main.nf → modules/nf-core/bedtools/genomecov/main.nf

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0 modules/bedtools/genomecov/meta.yml → modules/nf-core/bedtools/genomecov/meta.yml

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0 modules/bedtools/getfasta/main.nf → modules/nf-core/bedtools/getfasta/main.nf

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0 modules/bedtools/getfasta/meta.yml → modules/nf-core/bedtools/getfasta/meta.yml

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0 modules/bedtools/intersect/main.nf → modules/nf-core/bedtools/intersect/main.nf

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0 modules/bedtools/intersect/meta.yml → modules/nf-core/bedtools/intersect/meta.yml

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0 modules/bedtools/makewindows/main.nf → modules/nf-core/bedtools/makewindows/main.nf

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0 modules/bedtools/makewindows/meta.yml → ...les/nf-core/bedtools/makewindows/meta.yml

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0 modules/bedtools/maskfasta/main.nf → modules/nf-core/bedtools/maskfasta/main.nf

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0 modules/bedtools/maskfasta/meta.yml → modules/nf-core/bedtools/maskfasta/meta.yml

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0 modules/bedtools/merge/main.nf → modules/nf-core/bedtools/merge/main.nf

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0 modules/bedtools/merge/meta.yml → modules/nf-core/bedtools/merge/meta.yml

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0 modules/bedtools/slop/main.nf → modules/nf-core/bedtools/slop/main.nf

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0 modules/bedtools/slop/meta.yml → modules/nf-core/bedtools/slop/meta.yml

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0 modules/bedtools/sort/main.nf → modules/nf-core/bedtools/sort/main.nf

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0 modules/bedtools/sort/meta.yml → modules/nf-core/bedtools/sort/meta.yml

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0 modules/bedtools/split/main.nf → modules/nf-core/bedtools/split/main.nf

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0 modules/bedtools/split/meta.yml → modules/nf-core/bedtools/split/meta.yml

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0 modules/bedtools/subtract/main.nf → modules/nf-core/bedtools/subtract/main.nf

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0 modules/bedtools/subtract/meta.yml → modules/nf-core/bedtools/subtract/meta.yml

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0 modules/biobambam/bammarkduplicates2/main.nf → ...core/biobambam/bammarkduplicates2/main.nf

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0 ...les/biobambam/bammarkduplicates2/meta.yml → ...ore/biobambam/bammarkduplicates2/meta.yml

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0 modules/biobambam/bammerge/main.nf → modules/nf-core/biobambam/bammerge/main.nf

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0 modules/biobambam/bammerge/meta.yml → modules/nf-core/biobambam/bammerge/meta.yml

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0 modules/biobambam/bamsormadup/main.nf → ...les/nf-core/biobambam/bamsormadup/main.nf

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0 modules/biobambam/bamsormadup/meta.yml → ...es/nf-core/biobambam/bamsormadup/meta.yml

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0 modules/biscuit/align/main.nf → modules/nf-core/biscuit/align/main.nf

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0 modules/biscuit/align/meta.yml → modules/nf-core/biscuit/align/meta.yml

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0 modules/biscuit/biscuitblaster/main.nf → ...es/nf-core/biscuit/biscuitblaster/main.nf

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0 modules/biscuit/biscuitblaster/meta.yml → ...s/nf-core/biscuit/biscuitblaster/meta.yml

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0 modules/biscuit/bsconv/main.nf → modules/nf-core/biscuit/bsconv/main.nf

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0 modules/biscuit/bsconv/meta.yml → modules/nf-core/biscuit/bsconv/meta.yml

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0 modules/biscuit/epiread/main.nf → modules/nf-core/biscuit/epiread/main.nf

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0 modules/biscuit/epiread/meta.yml → modules/nf-core/biscuit/epiread/meta.yml

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0 modules/biscuit/index/main.nf → modules/nf-core/biscuit/index/main.nf

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0 modules/biscuit/index/meta.yml → modules/nf-core/biscuit/index/meta.yml

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0 modules/biscuit/mergecg/main.nf → modules/nf-core/biscuit/mergecg/main.nf

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0 modules/biscuit/mergecg/meta.yml → modules/nf-core/biscuit/mergecg/meta.yml

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0 modules/biscuit/pileup/main.nf → modules/nf-core/biscuit/pileup/main.nf

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0 modules/bismark/genomepreparation/main.nf → ...nf-core/bismark/genomepreparation/main.nf

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0 modules/bismark/methylationextractor/main.nf → ...core/bismark/methylationextractor/main.nf

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Restructure nf-core/modules repo #2141

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