Restructure nf-core/modules repo (#2141)

* Move all modules to modules/nf-core/ folder * Move all tests to modules/nf-core/ folder * Replace relative paths in modules test main scripts * Replace relative paths in subworkflow main scripts * Replace relative paths in subworkflow test scripts * Replace paths to tests in test.yml * Standardise path to tests/config to ./tests/config everywhere * Update relative paths in tests * Update paths in pytest_modules.yml Co-authored-by: Edmund Miller <[email protected]>
nf-core · Oct 4, 2022 · 5e34754 · 5e34754
1 parent bff70bd
commit 5e34754
Show file tree

Hide file tree

Showing 4,465 changed files with 33,612 additions and 33,612 deletions.
diff --git a/modules/abacas/main.nf → modules/nf-core/abacas/main.nf b/modules/abacas/main.nf → modules/nf-core/abacas/main.nf
diff --git a/modules/abacas/meta.yml → modules/nf-core/abacas/meta.yml b/modules/abacas/meta.yml → modules/nf-core/abacas/meta.yml
diff --git a/modules/abricate/run/main.nf → modules/nf-core/abricate/run/main.nf b/modules/abricate/run/main.nf → modules/nf-core/abricate/run/main.nf
diff --git a/modules/abricate/run/meta.yml → modules/nf-core/abricate/run/meta.yml b/modules/abricate/run/meta.yml → modules/nf-core/abricate/run/meta.yml
diff --git a/modules/abricate/summary/main.nf → modules/nf-core/abricate/summary/main.nf b/modules/abricate/summary/main.nf → modules/nf-core/abricate/summary/main.nf
diff --git a/modules/abricate/summary/meta.yml → modules/nf-core/abricate/summary/meta.yml b/modules/abricate/summary/meta.yml → modules/nf-core/abricate/summary/meta.yml
diff --git a/modules/adapterremoval/main.nf → modules/nf-core/adapterremoval/main.nf b/modules/adapterremoval/main.nf → modules/nf-core/adapterremoval/main.nf
diff --git a/modules/adapterremoval/meta.yml → modules/nf-core/adapterremoval/meta.yml b/modules/adapterremoval/meta.yml → modules/nf-core/adapterremoval/meta.yml
diff --git a/modules/adapterremovalfixprefix/main.nf → ...s/nf-core/adapterremovalfixprefix/main.nf b/modules/adapterremovalfixprefix/main.nf → ...s/nf-core/adapterremovalfixprefix/main.nf
diff --git a/modules/adapterremovalfixprefix/meta.yml → .../nf-core/adapterremovalfixprefix/meta.yml b/modules/adapterremovalfixprefix/meta.yml → .../nf-core/adapterremovalfixprefix/meta.yml
diff --git a/modules/agrvate/main.nf → modules/nf-core/agrvate/main.nf b/modules/agrvate/main.nf → modules/nf-core/agrvate/main.nf
diff --git a/modules/agrvate/meta.yml → modules/nf-core/agrvate/meta.yml b/modules/agrvate/meta.yml → modules/nf-core/agrvate/meta.yml
diff --git a/modules/allelecounter/main.nf → modules/nf-core/allelecounter/main.nf b/modules/allelecounter/main.nf → modules/nf-core/allelecounter/main.nf
diff --git a/modules/allelecounter/meta.yml → modules/nf-core/allelecounter/meta.yml b/modules/allelecounter/meta.yml → modules/nf-core/allelecounter/meta.yml
diff --git a/modules/ampir/main.nf → modules/nf-core/ampir/main.nf b/modules/ampir/main.nf → modules/nf-core/ampir/main.nf
diff --git a/modules/ampir/meta.yml → modules/nf-core/ampir/meta.yml b/modules/ampir/meta.yml → modules/nf-core/ampir/meta.yml
diff --git a/modules/amplify/predict/main.nf → modules/nf-core/amplify/predict/main.nf b/modules/amplify/predict/main.nf → modules/nf-core/amplify/predict/main.nf
diff --git a/modules/amplify/predict/meta.yml → modules/nf-core/amplify/predict/meta.yml b/modules/amplify/predict/meta.yml → modules/nf-core/amplify/predict/meta.yml
diff --git a/modules/amps/main.nf → modules/nf-core/amps/main.nf b/modules/amps/main.nf → modules/nf-core/amps/main.nf
diff --git a/modules/amps/meta.yml → modules/nf-core/amps/meta.yml b/modules/amps/meta.yml → modules/nf-core/amps/meta.yml
diff --git a/modules/amrfinderplus/run/main.nf → modules/nf-core/amrfinderplus/run/main.nf b/modules/amrfinderplus/run/main.nf → modules/nf-core/amrfinderplus/run/main.nf
diff --git a/modules/amrfinderplus/run/meta.yml → modules/nf-core/amrfinderplus/run/meta.yml b/modules/amrfinderplus/run/meta.yml → modules/nf-core/amrfinderplus/run/meta.yml
diff --git a/modules/amrfinderplus/update/main.nf → modules/nf-core/amrfinderplus/update/main.nf b/modules/amrfinderplus/update/main.nf → modules/nf-core/amrfinderplus/update/main.nf
diff --git a/modules/amrfinderplus/update/meta.yml → ...les/nf-core/amrfinderplus/update/meta.yml b/modules/amrfinderplus/update/meta.yml → ...les/nf-core/amrfinderplus/update/meta.yml
diff --git a/modules/angsd/docounts/main.nf → modules/nf-core/angsd/docounts/main.nf b/modules/angsd/docounts/main.nf → modules/nf-core/angsd/docounts/main.nf
diff --git a/modules/angsd/docounts/meta.yml → modules/nf-core/angsd/docounts/meta.yml b/modules/angsd/docounts/meta.yml → modules/nf-core/angsd/docounts/meta.yml
diff --git a/modules/antismash/antismashlite/main.nf → ...s/nf-core/antismash/antismashlite/main.nf b/modules/antismash/antismashlite/main.nf → ...s/nf-core/antismash/antismashlite/main.nf
diff --git a/modules/antismash/antismashlite/meta.yml → .../nf-core/antismash/antismashlite/meta.yml b/modules/antismash/antismashlite/meta.yml → .../nf-core/antismash/antismashlite/meta.yml
diff --git a/...sh/antismashlitedownloaddatabases/main.nf → ...sh/antismashlitedownloaddatabases/main.nf b/...sh/antismashlitedownloaddatabases/main.nf → ...sh/antismashlitedownloaddatabases/main.nf
diff --git a/...h/antismashlitedownloaddatabases/meta.yml → ...h/antismashlitedownloaddatabases/meta.yml b/...h/antismashlitedownloaddatabases/meta.yml → ...h/antismashlitedownloaddatabases/meta.yml
diff --git a/modules/ariba/getref/main.nf → modules/nf-core/ariba/getref/main.nf b/modules/ariba/getref/main.nf → modules/nf-core/ariba/getref/main.nf
diff --git a/modules/ariba/getref/meta.yml → modules/nf-core/ariba/getref/meta.yml b/modules/ariba/getref/meta.yml → modules/nf-core/ariba/getref/meta.yml
diff --git a/modules/ariba/run/main.nf → modules/nf-core/ariba/run/main.nf b/modules/ariba/run/main.nf → modules/nf-core/ariba/run/main.nf
diff --git a/modules/ariba/run/meta.yml → modules/nf-core/ariba/run/meta.yml b/modules/ariba/run/meta.yml → modules/nf-core/ariba/run/meta.yml
diff --git a/modules/arriba/main.nf → modules/nf-core/arriba/main.nf b/modules/arriba/main.nf → modules/nf-core/arriba/main.nf
diff --git a/modules/arriba/meta.yml → modules/nf-core/arriba/meta.yml b/modules/arriba/meta.yml → modules/nf-core/arriba/meta.yml
diff --git a/modules/artic/guppyplex/main.nf → modules/nf-core/artic/guppyplex/main.nf b/modules/artic/guppyplex/main.nf → modules/nf-core/artic/guppyplex/main.nf
diff --git a/modules/artic/guppyplex/meta.yml → modules/nf-core/artic/guppyplex/meta.yml b/modules/artic/guppyplex/meta.yml → modules/nf-core/artic/guppyplex/meta.yml
diff --git a/modules/artic/minion/main.nf → modules/nf-core/artic/minion/main.nf b/modules/artic/minion/main.nf → modules/nf-core/artic/minion/main.nf
diff --git a/modules/artic/minion/meta.yml → modules/nf-core/artic/minion/meta.yml b/modules/artic/minion/meta.yml → modules/nf-core/artic/minion/meta.yml
diff --git a/modules/ascat/main.nf → modules/nf-core/ascat/main.nf b/modules/ascat/main.nf → modules/nf-core/ascat/main.nf
diff --git a/modules/ascat/meta.yml → modules/nf-core/ascat/meta.yml b/modules/ascat/meta.yml → modules/nf-core/ascat/meta.yml
diff --git a/modules/assemblyscan/main.nf → modules/nf-core/assemblyscan/main.nf b/modules/assemblyscan/main.nf → modules/nf-core/assemblyscan/main.nf
diff --git a/modules/assemblyscan/meta.yml → modules/nf-core/assemblyscan/meta.yml b/modules/assemblyscan/meta.yml → modules/nf-core/assemblyscan/meta.yml
diff --git a/modules/ataqv/ataqv/main.nf → modules/nf-core/ataqv/ataqv/main.nf b/modules/ataqv/ataqv/main.nf → modules/nf-core/ataqv/ataqv/main.nf
diff --git a/modules/ataqv/ataqv/meta.yml → modules/nf-core/ataqv/ataqv/meta.yml b/modules/ataqv/ataqv/meta.yml → modules/nf-core/ataqv/ataqv/meta.yml
diff --git a/modules/ataqv/mkarv/main.nf → modules/nf-core/ataqv/mkarv/main.nf b/modules/ataqv/mkarv/main.nf → modules/nf-core/ataqv/mkarv/main.nf
diff --git a/modules/ataqv/mkarv/meta.yml → modules/nf-core/ataqv/mkarv/meta.yml b/modules/ataqv/mkarv/meta.yml → modules/nf-core/ataqv/mkarv/meta.yml
diff --git a/modules/atlas/call/main.nf → modules/nf-core/atlas/call/main.nf b/modules/atlas/call/main.nf → modules/nf-core/atlas/call/main.nf
diff --git a/modules/atlas/call/meta.yml → modules/nf-core/atlas/call/meta.yml b/modules/atlas/call/meta.yml → modules/nf-core/atlas/call/meta.yml
diff --git a/modules/atlas/pmd/main.nf → modules/nf-core/atlas/pmd/main.nf b/modules/atlas/pmd/main.nf → modules/nf-core/atlas/pmd/main.nf
diff --git a/modules/atlas/pmd/meta.yml → modules/nf-core/atlas/pmd/meta.yml b/modules/atlas/pmd/meta.yml → modules/nf-core/atlas/pmd/meta.yml
diff --git a/modules/atlas/recal/main.nf → modules/nf-core/atlas/recal/main.nf b/modules/atlas/recal/main.nf → modules/nf-core/atlas/recal/main.nf
diff --git a/modules/atlas/recal/meta.yml → modules/nf-core/atlas/recal/meta.yml b/modules/atlas/recal/meta.yml → modules/nf-core/atlas/recal/meta.yml
diff --git a/modules/atlas/splitmerge/main.nf → modules/nf-core/atlas/splitmerge/main.nf b/modules/atlas/splitmerge/main.nf → modules/nf-core/atlas/splitmerge/main.nf
diff --git a/modules/atlas/splitmerge/meta.yml → modules/nf-core/atlas/splitmerge/meta.yml b/modules/atlas/splitmerge/meta.yml → modules/nf-core/atlas/splitmerge/meta.yml
diff --git a/modules/bakta/main.nf → modules/nf-core/bakta/main.nf b/modules/bakta/main.nf → modules/nf-core/bakta/main.nf
diff --git a/modules/bakta/meta.yml → modules/nf-core/bakta/meta.yml b/modules/bakta/meta.yml → modules/nf-core/bakta/meta.yml
diff --git a/modules/bamaligncleaner/main.nf → modules/nf-core/bamaligncleaner/main.nf b/modules/bamaligncleaner/main.nf → modules/nf-core/bamaligncleaner/main.nf
diff --git a/modules/bamaligncleaner/meta.yml → modules/nf-core/bamaligncleaner/meta.yml b/modules/bamaligncleaner/meta.yml → modules/nf-core/bamaligncleaner/meta.yml
diff --git a/modules/bamcmp/main.nf → modules/nf-core/bamcmp/main.nf b/modules/bamcmp/main.nf → modules/nf-core/bamcmp/main.nf
diff --git a/modules/bamcmp/meta.yml → modules/nf-core/bamcmp/meta.yml b/modules/bamcmp/meta.yml → modules/nf-core/bamcmp/meta.yml
diff --git a/modules/bamtools/convert/main.nf → modules/nf-core/bamtools/convert/main.nf b/modules/bamtools/convert/main.nf → modules/nf-core/bamtools/convert/main.nf
diff --git a/modules/bamtools/convert/meta.yml → modules/nf-core/bamtools/convert/meta.yml b/modules/bamtools/convert/meta.yml → modules/nf-core/bamtools/convert/meta.yml
diff --git a/modules/bamtools/split/main.nf → modules/nf-core/bamtools/split/main.nf b/modules/bamtools/split/main.nf → modules/nf-core/bamtools/split/main.nf
diff --git a/modules/bamtools/split/meta.yml → modules/nf-core/bamtools/split/meta.yml b/modules/bamtools/split/meta.yml → modules/nf-core/bamtools/split/meta.yml
diff --git a/modules/bamtools/stats/main.nf → modules/nf-core/bamtools/stats/main.nf b/modules/bamtools/stats/main.nf → modules/nf-core/bamtools/stats/main.nf
diff --git a/modules/bamtools/stats/meta.yml → modules/nf-core/bamtools/stats/meta.yml b/modules/bamtools/stats/meta.yml → modules/nf-core/bamtools/stats/meta.yml
diff --git a/modules/bamutil/trimbam/main.nf → modules/nf-core/bamutil/trimbam/main.nf b/modules/bamutil/trimbam/main.nf → modules/nf-core/bamutil/trimbam/main.nf
diff --git a/modules/bamutil/trimbam/meta.yml → modules/nf-core/bamutil/trimbam/meta.yml b/modules/bamutil/trimbam/meta.yml → modules/nf-core/bamutil/trimbam/meta.yml
diff --git a/modules/bandage/image/main.nf → modules/nf-core/bandage/image/main.nf b/modules/bandage/image/main.nf → modules/nf-core/bandage/image/main.nf
diff --git a/modules/bandage/image/meta.yml → modules/nf-core/bandage/image/meta.yml b/modules/bandage/image/meta.yml → modules/nf-core/bandage/image/meta.yml
diff --git a/modules/bases2fastq/main.nf → modules/nf-core/bases2fastq/main.nf b/modules/bases2fastq/main.nf → modules/nf-core/bases2fastq/main.nf
diff --git a/modules/bases2fastq/meta.yml → modules/nf-core/bases2fastq/meta.yml b/modules/bases2fastq/meta.yml → modules/nf-core/bases2fastq/meta.yml
diff --git a/modules/bbmap/align/main.nf → modules/nf-core/bbmap/align/main.nf b/modules/bbmap/align/main.nf → modules/nf-core/bbmap/align/main.nf
diff --git a/modules/bbmap/align/meta.yml → modules/nf-core/bbmap/align/meta.yml b/modules/bbmap/align/meta.yml → modules/nf-core/bbmap/align/meta.yml
diff --git a/modules/bbmap/bbduk/main.nf → modules/nf-core/bbmap/bbduk/main.nf b/modules/bbmap/bbduk/main.nf → modules/nf-core/bbmap/bbduk/main.nf
diff --git a/modules/bbmap/bbduk/meta.yml → modules/nf-core/bbmap/bbduk/meta.yml b/modules/bbmap/bbduk/meta.yml → modules/nf-core/bbmap/bbduk/meta.yml
diff --git a/modules/bbmap/bbsplit/main.nf → modules/nf-core/bbmap/bbsplit/main.nf b/modules/bbmap/bbsplit/main.nf → modules/nf-core/bbmap/bbsplit/main.nf
diff --git a/modules/bbmap/bbsplit/meta.yml → modules/nf-core/bbmap/bbsplit/meta.yml b/modules/bbmap/bbsplit/meta.yml → modules/nf-core/bbmap/bbsplit/meta.yml
diff --git a/modules/bbmap/clumpify/main.nf → modules/nf-core/bbmap/clumpify/main.nf b/modules/bbmap/clumpify/main.nf → modules/nf-core/bbmap/clumpify/main.nf
diff --git a/modules/bbmap/clumpify/meta.yml → modules/nf-core/bbmap/clumpify/meta.yml b/modules/bbmap/clumpify/meta.yml → modules/nf-core/bbmap/clumpify/meta.yml
diff --git a/modules/bbmap/index/main.nf → modules/nf-core/bbmap/index/main.nf b/modules/bbmap/index/main.nf → modules/nf-core/bbmap/index/main.nf
diff --git a/modules/bbmap/index/meta.yml → modules/nf-core/bbmap/index/meta.yml b/modules/bbmap/index/meta.yml → modules/nf-core/bbmap/index/meta.yml
diff --git a/modules/bbmap/pileup/main.nf → modules/nf-core/bbmap/pileup/main.nf b/modules/bbmap/pileup/main.nf → modules/nf-core/bbmap/pileup/main.nf
diff --git a/modules/bbmap/pileup/meta.yml → modules/nf-core/bbmap/pileup/meta.yml b/modules/bbmap/pileup/meta.yml → modules/nf-core/bbmap/pileup/meta.yml
diff --git a/modules/bcftools/annotate/main.nf → modules/nf-core/bcftools/annotate/main.nf b/modules/bcftools/annotate/main.nf → modules/nf-core/bcftools/annotate/main.nf
diff --git a/modules/bcftools/annotate/meta.yml → modules/nf-core/bcftools/annotate/meta.yml b/modules/bcftools/annotate/meta.yml → modules/nf-core/bcftools/annotate/meta.yml
diff --git a/modules/bcftools/concat/main.nf → modules/nf-core/bcftools/concat/main.nf b/modules/bcftools/concat/main.nf → modules/nf-core/bcftools/concat/main.nf
diff --git a/modules/bcftools/concat/meta.yml → modules/nf-core/bcftools/concat/meta.yml b/modules/bcftools/concat/meta.yml → modules/nf-core/bcftools/concat/meta.yml
diff --git a/modules/bcftools/consensus/main.nf → modules/nf-core/bcftools/consensus/main.nf b/modules/bcftools/consensus/main.nf → modules/nf-core/bcftools/consensus/main.nf
diff --git a/modules/bcftools/consensus/meta.yml → modules/nf-core/bcftools/consensus/meta.yml b/modules/bcftools/consensus/meta.yml → modules/nf-core/bcftools/consensus/meta.yml
diff --git a/modules/bcftools/convert/main.nf → modules/nf-core/bcftools/convert/main.nf b/modules/bcftools/convert/main.nf → modules/nf-core/bcftools/convert/main.nf
diff --git a/modules/bcftools/convert/meta.yml → modules/nf-core/bcftools/convert/meta.yml b/modules/bcftools/convert/meta.yml → modules/nf-core/bcftools/convert/meta.yml
diff --git a/modules/bcftools/filter/main.nf → modules/nf-core/bcftools/filter/main.nf b/modules/bcftools/filter/main.nf → modules/nf-core/bcftools/filter/main.nf
diff --git a/modules/bcftools/filter/meta.yml → modules/nf-core/bcftools/filter/meta.yml b/modules/bcftools/filter/meta.yml → modules/nf-core/bcftools/filter/meta.yml
diff --git a/modules/bcftools/index/main.nf → modules/nf-core/bcftools/index/main.nf b/modules/bcftools/index/main.nf → modules/nf-core/bcftools/index/main.nf
diff --git a/modules/bcftools/index/meta.yml → modules/nf-core/bcftools/index/meta.yml b/modules/bcftools/index/meta.yml → modules/nf-core/bcftools/index/meta.yml
diff --git a/modules/bcftools/isec/main.nf → modules/nf-core/bcftools/isec/main.nf b/modules/bcftools/isec/main.nf → modules/nf-core/bcftools/isec/main.nf
diff --git a/modules/bcftools/isec/meta.yml → modules/nf-core/bcftools/isec/meta.yml b/modules/bcftools/isec/meta.yml → modules/nf-core/bcftools/isec/meta.yml
diff --git a/modules/bcftools/merge/main.nf → modules/nf-core/bcftools/merge/main.nf b/modules/bcftools/merge/main.nf → modules/nf-core/bcftools/merge/main.nf
diff --git a/modules/bcftools/merge/meta.yml → modules/nf-core/bcftools/merge/meta.yml b/modules/bcftools/merge/meta.yml → modules/nf-core/bcftools/merge/meta.yml
diff --git a/modules/bcftools/mpileup/main.nf → modules/nf-core/bcftools/mpileup/main.nf b/modules/bcftools/mpileup/main.nf → modules/nf-core/bcftools/mpileup/main.nf
diff --git a/modules/bcftools/mpileup/meta.yml → modules/nf-core/bcftools/mpileup/meta.yml b/modules/bcftools/mpileup/meta.yml → modules/nf-core/bcftools/mpileup/meta.yml
diff --git a/modules/bcftools/norm/main.nf → modules/nf-core/bcftools/norm/main.nf b/modules/bcftools/norm/main.nf → modules/nf-core/bcftools/norm/main.nf
diff --git a/modules/bcftools/norm/meta.yml → modules/nf-core/bcftools/norm/meta.yml b/modules/bcftools/norm/meta.yml → modules/nf-core/bcftools/norm/meta.yml
diff --git a/modules/bcftools/query/main.nf → modules/nf-core/bcftools/query/main.nf b/modules/bcftools/query/main.nf → modules/nf-core/bcftools/query/main.nf
diff --git a/modules/bcftools/query/meta.yml → modules/nf-core/bcftools/query/meta.yml b/modules/bcftools/query/meta.yml → modules/nf-core/bcftools/query/meta.yml
diff --git a/modules/bcftools/reheader/main.nf → modules/nf-core/bcftools/reheader/main.nf b/modules/bcftools/reheader/main.nf → modules/nf-core/bcftools/reheader/main.nf
diff --git a/modules/bcftools/reheader/meta.yml → modules/nf-core/bcftools/reheader/meta.yml b/modules/bcftools/reheader/meta.yml → modules/nf-core/bcftools/reheader/meta.yml
diff --git a/modules/bcftools/roh/main.nf → modules/nf-core/bcftools/roh/main.nf b/modules/bcftools/roh/main.nf → modules/nf-core/bcftools/roh/main.nf
diff --git a/modules/bcftools/roh/meta.yml → modules/nf-core/bcftools/roh/meta.yml b/modules/bcftools/roh/meta.yml → modules/nf-core/bcftools/roh/meta.yml
diff --git a/modules/bcftools/sort/main.nf → modules/nf-core/bcftools/sort/main.nf b/modules/bcftools/sort/main.nf → modules/nf-core/bcftools/sort/main.nf
diff --git a/modules/bcftools/sort/meta.yml → modules/nf-core/bcftools/sort/meta.yml b/modules/bcftools/sort/meta.yml → modules/nf-core/bcftools/sort/meta.yml
diff --git a/modules/bcftools/stats/main.nf → modules/nf-core/bcftools/stats/main.nf b/modules/bcftools/stats/main.nf → modules/nf-core/bcftools/stats/main.nf
diff --git a/modules/bcftools/stats/meta.yml → modules/nf-core/bcftools/stats/meta.yml b/modules/bcftools/stats/meta.yml → modules/nf-core/bcftools/stats/meta.yml
diff --git a/modules/bcftools/view/main.nf → modules/nf-core/bcftools/view/main.nf b/modules/bcftools/view/main.nf → modules/nf-core/bcftools/view/main.nf
diff --git a/modules/bcftools/view/meta.yml → modules/nf-core/bcftools/view/meta.yml b/modules/bcftools/view/meta.yml → modules/nf-core/bcftools/view/meta.yml
diff --git a/modules/bcl2fastq/.gitignore → modules/nf-core/bcl2fastq/.gitignore b/modules/bcl2fastq/.gitignore → modules/nf-core/bcl2fastq/.gitignore
diff --git a/modules/bcl2fastq/Dockerfile → modules/nf-core/bcl2fastq/Dockerfile b/modules/bcl2fastq/Dockerfile → modules/nf-core/bcl2fastq/Dockerfile
diff --git a/modules/bcl2fastq/LICENSE → modules/nf-core/bcl2fastq/LICENSE b/modules/bcl2fastq/LICENSE → modules/nf-core/bcl2fastq/LICENSE
diff --git a/modules/bcl2fastq/README.md → modules/nf-core/bcl2fastq/README.md b/modules/bcl2fastq/README.md → modules/nf-core/bcl2fastq/README.md
diff --git a/modules/bcl2fastq/main.nf → modules/nf-core/bcl2fastq/main.nf b/modules/bcl2fastq/main.nf → modules/nf-core/bcl2fastq/main.nf
diff --git a/modules/bcl2fastq/meta.yml → modules/nf-core/bcl2fastq/meta.yml b/modules/bcl2fastq/meta.yml → modules/nf-core/bcl2fastq/meta.yml
diff --git a/modules/bclconvert/.gitignore → modules/nf-core/bclconvert/.gitignore b/modules/bclconvert/.gitignore → modules/nf-core/bclconvert/.gitignore
diff --git a/modules/bclconvert/Dockerfile → modules/nf-core/bclconvert/Dockerfile b/modules/bclconvert/Dockerfile → modules/nf-core/bclconvert/Dockerfile
diff --git a/modules/bclconvert/LICENSE → modules/nf-core/bclconvert/LICENSE b/modules/bclconvert/LICENSE → modules/nf-core/bclconvert/LICENSE
diff --git a/modules/bclconvert/README.md → modules/nf-core/bclconvert/README.md b/modules/bclconvert/README.md → modules/nf-core/bclconvert/README.md
diff --git a/modules/bclconvert/main.nf → modules/nf-core/bclconvert/main.nf b/modules/bclconvert/main.nf → modules/nf-core/bclconvert/main.nf
diff --git a/modules/bclconvert/meta.yml → modules/nf-core/bclconvert/meta.yml b/modules/bclconvert/meta.yml → modules/nf-core/bclconvert/meta.yml
diff --git a/modules/bedtools/bamtobed/main.nf → modules/nf-core/bedtools/bamtobed/main.nf b/modules/bedtools/bamtobed/main.nf → modules/nf-core/bedtools/bamtobed/main.nf
diff --git a/modules/bedtools/bamtobed/meta.yml → modules/nf-core/bedtools/bamtobed/meta.yml b/modules/bedtools/bamtobed/meta.yml → modules/nf-core/bedtools/bamtobed/meta.yml
diff --git a/modules/bedtools/complement/main.nf → modules/nf-core/bedtools/complement/main.nf b/modules/bedtools/complement/main.nf → modules/nf-core/bedtools/complement/main.nf
diff --git a/modules/bedtools/complement/meta.yml → modules/nf-core/bedtools/complement/meta.yml b/modules/bedtools/complement/meta.yml → modules/nf-core/bedtools/complement/meta.yml
diff --git a/modules/bedtools/genomecov/main.nf → modules/nf-core/bedtools/genomecov/main.nf b/modules/bedtools/genomecov/main.nf → modules/nf-core/bedtools/genomecov/main.nf
diff --git a/modules/bedtools/genomecov/meta.yml → modules/nf-core/bedtools/genomecov/meta.yml b/modules/bedtools/genomecov/meta.yml → modules/nf-core/bedtools/genomecov/meta.yml
diff --git a/modules/bedtools/getfasta/main.nf → modules/nf-core/bedtools/getfasta/main.nf b/modules/bedtools/getfasta/main.nf → modules/nf-core/bedtools/getfasta/main.nf
diff --git a/modules/bedtools/getfasta/meta.yml → modules/nf-core/bedtools/getfasta/meta.yml b/modules/bedtools/getfasta/meta.yml → modules/nf-core/bedtools/getfasta/meta.yml
diff --git a/modules/bedtools/intersect/main.nf → modules/nf-core/bedtools/intersect/main.nf b/modules/bedtools/intersect/main.nf → modules/nf-core/bedtools/intersect/main.nf
diff --git a/modules/bedtools/intersect/meta.yml → modules/nf-core/bedtools/intersect/meta.yml b/modules/bedtools/intersect/meta.yml → modules/nf-core/bedtools/intersect/meta.yml
diff --git a/modules/bedtools/makewindows/main.nf → modules/nf-core/bedtools/makewindows/main.nf b/modules/bedtools/makewindows/main.nf → modules/nf-core/bedtools/makewindows/main.nf
diff --git a/modules/bedtools/makewindows/meta.yml → ...les/nf-core/bedtools/makewindows/meta.yml b/modules/bedtools/makewindows/meta.yml → ...les/nf-core/bedtools/makewindows/meta.yml
diff --git a/modules/bedtools/maskfasta/main.nf → modules/nf-core/bedtools/maskfasta/main.nf b/modules/bedtools/maskfasta/main.nf → modules/nf-core/bedtools/maskfasta/main.nf
diff --git a/modules/bedtools/maskfasta/meta.yml → modules/nf-core/bedtools/maskfasta/meta.yml b/modules/bedtools/maskfasta/meta.yml → modules/nf-core/bedtools/maskfasta/meta.yml
diff --git a/modules/bedtools/merge/main.nf → modules/nf-core/bedtools/merge/main.nf b/modules/bedtools/merge/main.nf → modules/nf-core/bedtools/merge/main.nf
diff --git a/modules/bedtools/merge/meta.yml → modules/nf-core/bedtools/merge/meta.yml b/modules/bedtools/merge/meta.yml → modules/nf-core/bedtools/merge/meta.yml
diff --git a/modules/bedtools/slop/main.nf → modules/nf-core/bedtools/slop/main.nf b/modules/bedtools/slop/main.nf → modules/nf-core/bedtools/slop/main.nf
diff --git a/modules/bedtools/slop/meta.yml → modules/nf-core/bedtools/slop/meta.yml b/modules/bedtools/slop/meta.yml → modules/nf-core/bedtools/slop/meta.yml
diff --git a/modules/bedtools/sort/main.nf → modules/nf-core/bedtools/sort/main.nf b/modules/bedtools/sort/main.nf → modules/nf-core/bedtools/sort/main.nf
diff --git a/modules/bedtools/sort/meta.yml → modules/nf-core/bedtools/sort/meta.yml b/modules/bedtools/sort/meta.yml → modules/nf-core/bedtools/sort/meta.yml
diff --git a/modules/bedtools/split/main.nf → modules/nf-core/bedtools/split/main.nf b/modules/bedtools/split/main.nf → modules/nf-core/bedtools/split/main.nf
diff --git a/modules/bedtools/split/meta.yml → modules/nf-core/bedtools/split/meta.yml b/modules/bedtools/split/meta.yml → modules/nf-core/bedtools/split/meta.yml
diff --git a/modules/bedtools/subtract/main.nf → modules/nf-core/bedtools/subtract/main.nf b/modules/bedtools/subtract/main.nf → modules/nf-core/bedtools/subtract/main.nf
diff --git a/modules/bedtools/subtract/meta.yml → modules/nf-core/bedtools/subtract/meta.yml b/modules/bedtools/subtract/meta.yml → modules/nf-core/bedtools/subtract/meta.yml
diff --git a/modules/biobambam/bammarkduplicates2/main.nf → ...core/biobambam/bammarkduplicates2/main.nf b/modules/biobambam/bammarkduplicates2/main.nf → ...core/biobambam/bammarkduplicates2/main.nf
diff --git a/...les/biobambam/bammarkduplicates2/meta.yml → ...ore/biobambam/bammarkduplicates2/meta.yml b/...les/biobambam/bammarkduplicates2/meta.yml → ...ore/biobambam/bammarkduplicates2/meta.yml
diff --git a/modules/biobambam/bammerge/main.nf → modules/nf-core/biobambam/bammerge/main.nf b/modules/biobambam/bammerge/main.nf → modules/nf-core/biobambam/bammerge/main.nf
diff --git a/modules/biobambam/bammerge/meta.yml → modules/nf-core/biobambam/bammerge/meta.yml b/modules/biobambam/bammerge/meta.yml → modules/nf-core/biobambam/bammerge/meta.yml
diff --git a/modules/biobambam/bamsormadup/main.nf → ...les/nf-core/biobambam/bamsormadup/main.nf b/modules/biobambam/bamsormadup/main.nf → ...les/nf-core/biobambam/bamsormadup/main.nf
diff --git a/modules/biobambam/bamsormadup/meta.yml → ...es/nf-core/biobambam/bamsormadup/meta.yml b/modules/biobambam/bamsormadup/meta.yml → ...es/nf-core/biobambam/bamsormadup/meta.yml
diff --git a/modules/biscuit/align/main.nf → modules/nf-core/biscuit/align/main.nf b/modules/biscuit/align/main.nf → modules/nf-core/biscuit/align/main.nf
diff --git a/modules/biscuit/align/meta.yml → modules/nf-core/biscuit/align/meta.yml b/modules/biscuit/align/meta.yml → modules/nf-core/biscuit/align/meta.yml
diff --git a/modules/biscuit/biscuitblaster/main.nf → ...es/nf-core/biscuit/biscuitblaster/main.nf b/modules/biscuit/biscuitblaster/main.nf → ...es/nf-core/biscuit/biscuitblaster/main.nf
diff --git a/modules/biscuit/biscuitblaster/meta.yml → ...s/nf-core/biscuit/biscuitblaster/meta.yml b/modules/biscuit/biscuitblaster/meta.yml → ...s/nf-core/biscuit/biscuitblaster/meta.yml
diff --git a/modules/biscuit/bsconv/main.nf → modules/nf-core/biscuit/bsconv/main.nf b/modules/biscuit/bsconv/main.nf → modules/nf-core/biscuit/bsconv/main.nf
diff --git a/modules/biscuit/bsconv/meta.yml → modules/nf-core/biscuit/bsconv/meta.yml b/modules/biscuit/bsconv/meta.yml → modules/nf-core/biscuit/bsconv/meta.yml
diff --git a/modules/biscuit/epiread/main.nf → modules/nf-core/biscuit/epiread/main.nf b/modules/biscuit/epiread/main.nf → modules/nf-core/biscuit/epiread/main.nf
diff --git a/modules/biscuit/epiread/meta.yml → modules/nf-core/biscuit/epiread/meta.yml b/modules/biscuit/epiread/meta.yml → modules/nf-core/biscuit/epiread/meta.yml
diff --git a/modules/biscuit/index/main.nf → modules/nf-core/biscuit/index/main.nf b/modules/biscuit/index/main.nf → modules/nf-core/biscuit/index/main.nf
diff --git a/modules/biscuit/index/meta.yml → modules/nf-core/biscuit/index/meta.yml b/modules/biscuit/index/meta.yml → modules/nf-core/biscuit/index/meta.yml
diff --git a/modules/biscuit/mergecg/main.nf → modules/nf-core/biscuit/mergecg/main.nf b/modules/biscuit/mergecg/main.nf → modules/nf-core/biscuit/mergecg/main.nf
diff --git a/modules/biscuit/mergecg/meta.yml → modules/nf-core/biscuit/mergecg/meta.yml b/modules/biscuit/mergecg/meta.yml → modules/nf-core/biscuit/mergecg/meta.yml
diff --git a/modules/biscuit/pileup/main.nf → modules/nf-core/biscuit/pileup/main.nf b/modules/biscuit/pileup/main.nf → modules/nf-core/biscuit/pileup/main.nf
diff --git a/modules/biscuit/pileup/meta.yml → modules/nf-core/biscuit/pileup/meta.yml b/modules/biscuit/pileup/meta.yml → modules/nf-core/biscuit/pileup/meta.yml
diff --git a/modules/biscuit/qc/main.nf → modules/nf-core/biscuit/qc/main.nf b/modules/biscuit/qc/main.nf → modules/nf-core/biscuit/qc/main.nf
diff --git a/modules/biscuit/qc/meta.yml → modules/nf-core/biscuit/qc/meta.yml b/modules/biscuit/qc/meta.yml → modules/nf-core/biscuit/qc/meta.yml
diff --git a/modules/biscuit/vcf2bed/main.nf → modules/nf-core/biscuit/vcf2bed/main.nf b/modules/biscuit/vcf2bed/main.nf → modules/nf-core/biscuit/vcf2bed/main.nf
diff --git a/modules/biscuit/vcf2bed/meta.yml → modules/nf-core/biscuit/vcf2bed/meta.yml b/modules/biscuit/vcf2bed/meta.yml → modules/nf-core/biscuit/vcf2bed/meta.yml
diff --git a/modules/bismark/align/main.nf → modules/nf-core/bismark/align/main.nf b/modules/bismark/align/main.nf → modules/nf-core/bismark/align/main.nf
diff --git a/modules/bismark/align/meta.yml → modules/nf-core/bismark/align/meta.yml b/modules/bismark/align/meta.yml → modules/nf-core/bismark/align/meta.yml
diff --git a/modules/bismark/deduplicate/main.nf → modules/nf-core/bismark/deduplicate/main.nf b/modules/bismark/deduplicate/main.nf → modules/nf-core/bismark/deduplicate/main.nf
diff --git a/modules/bismark/deduplicate/meta.yml → modules/nf-core/bismark/deduplicate/meta.yml b/modules/bismark/deduplicate/meta.yml → modules/nf-core/bismark/deduplicate/meta.yml
diff --git a/modules/bismark/genomepreparation/main.nf → ...nf-core/bismark/genomepreparation/main.nf b/modules/bismark/genomepreparation/main.nf → ...nf-core/bismark/genomepreparation/main.nf
diff --git a/modules/bismark/genomepreparation/meta.yml → ...f-core/bismark/genomepreparation/meta.yml b/modules/bismark/genomepreparation/meta.yml → ...f-core/bismark/genomepreparation/meta.yml
diff --git a/modules/bismark/methylationextractor/main.nf → ...core/bismark/methylationextractor/main.nf b/modules/bismark/methylationextractor/main.nf → ...core/bismark/methylationextractor/main.nf
diff --git a/...les/bismark/methylationextractor/meta.yml → ...ore/bismark/methylationextractor/meta.yml b/...les/bismark/methylationextractor/meta.yml → ...ore/bismark/methylationextractor/meta.yml
diff --git a/modules/bismark/report/main.nf → modules/nf-core/bismark/report/main.nf b/modules/bismark/report/main.nf → modules/nf-core/bismark/report/main.nf
diff --git a/modules/bismark/report/meta.yml → modules/nf-core/bismark/report/meta.yml b/modules/bismark/report/meta.yml → modules/nf-core/bismark/report/meta.yml
diff --git a/modules/bismark/summary/main.nf → modules/nf-core/bismark/summary/main.nf b/modules/bismark/summary/main.nf → modules/nf-core/bismark/summary/main.nf
diff --git a/modules/bismark/summary/meta.yml → modules/nf-core/bismark/summary/meta.yml b/modules/bismark/summary/meta.yml → modules/nf-core/bismark/summary/meta.yml
diff --git a/modules/blast/blastn/main.nf → modules/nf-core/blast/blastn/main.nf b/modules/blast/blastn/main.nf → modules/nf-core/blast/blastn/main.nf
diff --git a/modules/blast/blastn/meta.yml → modules/nf-core/blast/blastn/meta.yml b/modules/blast/blastn/meta.yml → modules/nf-core/blast/blastn/meta.yml
diff --git a/modules/blast/makeblastdb/main.nf → modules/nf-core/blast/makeblastdb/main.nf b/modules/blast/makeblastdb/main.nf → modules/nf-core/blast/makeblastdb/main.nf
diff --git a/modules/blast/makeblastdb/meta.yml → modules/nf-core/blast/makeblastdb/meta.yml b/modules/blast/makeblastdb/meta.yml → modules/nf-core/blast/makeblastdb/meta.yml
diff --git a/modules/blast/tblastn/main.nf → modules/nf-core/blast/tblastn/main.nf b/modules/blast/tblastn/main.nf → modules/nf-core/blast/tblastn/main.nf
diff --git a/modules/blast/tblastn/meta.yml → modules/nf-core/blast/tblastn/meta.yml b/modules/blast/tblastn/meta.yml → modules/nf-core/blast/tblastn/meta.yml
diff --git a/modules/bowtie/align/main.nf → modules/nf-core/bowtie/align/main.nf b/modules/bowtie/align/main.nf → modules/nf-core/bowtie/align/main.nf
diff --git a/modules/bowtie/align/meta.yml → modules/nf-core/bowtie/align/meta.yml b/modules/bowtie/align/meta.yml → modules/nf-core/bowtie/align/meta.yml
diff --git a/modules/bowtie/build/main.nf → modules/nf-core/bowtie/build/main.nf b/modules/bowtie/build/main.nf → modules/nf-core/bowtie/build/main.nf
diff --git a/modules/bowtie/build/meta.yml → modules/nf-core/bowtie/build/meta.yml b/modules/bowtie/build/meta.yml → modules/nf-core/bowtie/build/meta.yml
diff --git a/modules/bowtie2/align/main.nf → modules/nf-core/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf → modules/nf-core/bowtie2/align/main.nf
diff --git a/modules/bowtie2/align/meta.yml → modules/nf-core/bowtie2/align/meta.yml b/modules/bowtie2/align/meta.yml → modules/nf-core/bowtie2/align/meta.yml
diff --git a/modules/bowtie2/build/main.nf → modules/nf-core/bowtie2/build/main.nf b/modules/bowtie2/build/main.nf → modules/nf-core/bowtie2/build/main.nf
diff --git a/modules/bowtie2/build/meta.yml → modules/nf-core/bowtie2/build/meta.yml b/modules/bowtie2/build/meta.yml → modules/nf-core/bowtie2/build/meta.yml
diff --git a/modules/bracken/bracken/main.nf → modules/nf-core/bracken/bracken/main.nf b/modules/bracken/bracken/main.nf → modules/nf-core/bracken/bracken/main.nf
diff --git a/modules/bracken/bracken/meta.yml → modules/nf-core/bracken/bracken/meta.yml b/modules/bracken/bracken/meta.yml → modules/nf-core/bracken/bracken/meta.yml
diff --git a/...les/bracken/combinebrackenoutputs/main.nf → ...ore/bracken/combinebrackenoutputs/main.nf b/...les/bracken/combinebrackenoutputs/main.nf → ...ore/bracken/combinebrackenoutputs/main.nf
diff --git a/...es/bracken/combinebrackenoutputs/meta.yml → ...re/bracken/combinebrackenoutputs/meta.yml b/...es/bracken/combinebrackenoutputs/meta.yml → ...re/bracken/combinebrackenoutputs/meta.yml
diff --git a/modules/busco/main.nf → modules/nf-core/busco/main.nf b/modules/busco/main.nf → modules/nf-core/busco/main.nf
diff --git a/modules/busco/meta.yml → modules/nf-core/busco/meta.yml b/modules/busco/meta.yml → modules/nf-core/busco/meta.yml
diff --git a/modules/bwa/aln/main.nf → modules/nf-core/bwa/aln/main.nf b/modules/bwa/aln/main.nf → modules/nf-core/bwa/aln/main.nf
diff --git a/modules/bwa/aln/meta.yml → modules/nf-core/bwa/aln/meta.yml b/modules/bwa/aln/meta.yml → modules/nf-core/bwa/aln/meta.yml
diff --git a/modules/bwa/index/main.nf → modules/nf-core/bwa/index/main.nf b/modules/bwa/index/main.nf → modules/nf-core/bwa/index/main.nf
diff --git a/modules/bwa/index/meta.yml → modules/nf-core/bwa/index/meta.yml b/modules/bwa/index/meta.yml → modules/nf-core/bwa/index/meta.yml
diff --git a/modules/bwa/mem/main.nf → modules/nf-core/bwa/mem/main.nf b/modules/bwa/mem/main.nf → modules/nf-core/bwa/mem/main.nf
diff --git a/modules/bwa/mem/meta.yml → modules/nf-core/bwa/mem/meta.yml b/modules/bwa/mem/meta.yml → modules/nf-core/bwa/mem/meta.yml
diff --git a/modules/bwa/sampe/main.nf → modules/nf-core/bwa/sampe/main.nf b/modules/bwa/sampe/main.nf → modules/nf-core/bwa/sampe/main.nf
diff --git a/modules/bwa/sampe/meta.yml → modules/nf-core/bwa/sampe/meta.yml b/modules/bwa/sampe/meta.yml → modules/nf-core/bwa/sampe/meta.yml
diff --git a/modules/bwa/samse/main.nf → modules/nf-core/bwa/samse/main.nf b/modules/bwa/samse/main.nf → modules/nf-core/bwa/samse/main.nf
diff --git a/modules/bwa/samse/meta.yml → modules/nf-core/bwa/samse/meta.yml b/modules/bwa/samse/meta.yml → modules/nf-core/bwa/samse/meta.yml
diff --git a/modules/bwamem2/index/main.nf → modules/nf-core/bwamem2/index/main.nf b/modules/bwamem2/index/main.nf → modules/nf-core/bwamem2/index/main.nf
diff --git a/modules/bwamem2/index/meta.yml → modules/nf-core/bwamem2/index/meta.yml b/modules/bwamem2/index/meta.yml → modules/nf-core/bwamem2/index/meta.yml
diff --git a/modules/bwamem2/mem/main.nf → modules/nf-core/bwamem2/mem/main.nf b/modules/bwamem2/mem/main.nf → modules/nf-core/bwamem2/mem/main.nf
diff --git a/modules/bwamem2/mem/meta.yml → modules/nf-core/bwamem2/mem/meta.yml b/modules/bwamem2/mem/meta.yml → modules/nf-core/bwamem2/mem/meta.yml
diff --git a/modules/bwameth/align/main.nf → modules/nf-core/bwameth/align/main.nf b/modules/bwameth/align/main.nf → modules/nf-core/bwameth/align/main.nf
diff --git a/modules/bwameth/align/meta.yml → modules/nf-core/bwameth/align/meta.yml b/modules/bwameth/align/meta.yml → modules/nf-core/bwameth/align/meta.yml
diff --git a/modules/bwameth/index/main.nf → modules/nf-core/bwameth/index/main.nf b/modules/bwameth/index/main.nf → modules/nf-core/bwameth/index/main.nf
diff --git a/modules/bwameth/index/meta.yml → modules/nf-core/bwameth/index/meta.yml b/modules/bwameth/index/meta.yml → modules/nf-core/bwameth/index/meta.yml
diff --git a/modules/cat/cat/main.nf → modules/nf-core/cat/cat/main.nf b/modules/cat/cat/main.nf → modules/nf-core/cat/cat/main.nf
diff --git a/modules/cat/cat/meta.yml → modules/nf-core/cat/cat/meta.yml b/modules/cat/cat/meta.yml → modules/nf-core/cat/cat/meta.yml
diff --git a/modules/cat/fastq/main.nf → modules/nf-core/cat/fastq/main.nf b/modules/cat/fastq/main.nf → modules/nf-core/cat/fastq/main.nf
diff --git a/modules/cat/fastq/meta.yml → modules/nf-core/cat/fastq/meta.yml b/modules/cat/fastq/meta.yml → modules/nf-core/cat/fastq/meta.yml
diff --git a/modules/cellranger/.gitignore → modules/nf-core/cellranger/.gitignore b/modules/cellranger/.gitignore → modules/nf-core/cellranger/.gitignore
diff --git a/modules/cellranger/Dockerfile → modules/nf-core/cellranger/Dockerfile b/modules/cellranger/Dockerfile → modules/nf-core/cellranger/Dockerfile
diff --git a/modules/cellranger/README.md → modules/nf-core/cellranger/README.md b/modules/cellranger/README.md → modules/nf-core/cellranger/README.md
diff --git a/modules/cellranger/count/main.nf → modules/nf-core/cellranger/count/main.nf b/modules/cellranger/count/main.nf → modules/nf-core/cellranger/count/main.nf
diff --git a/modules/cellranger/count/meta.yml → modules/nf-core/cellranger/count/meta.yml b/modules/cellranger/count/meta.yml → modules/nf-core/cellranger/count/meta.yml
diff --git a/modules/cellranger/mkfastq/Dockerfile → ...les/nf-core/cellranger/mkfastq/Dockerfile b/modules/cellranger/mkfastq/Dockerfile → ...les/nf-core/cellranger/mkfastq/Dockerfile
diff --git a/modules/cellranger/mkfastq/README.md → modules/nf-core/cellranger/mkfastq/README.md b/modules/cellranger/mkfastq/README.md → modules/nf-core/cellranger/mkfastq/README.md
diff --git a/modules/cellranger/mkfastq/main.nf → modules/nf-core/cellranger/mkfastq/main.nf b/modules/cellranger/mkfastq/main.nf → modules/nf-core/cellranger/mkfastq/main.nf
diff --git a/modules/cellranger/mkfastq/meta.yml → modules/nf-core/cellranger/mkfastq/meta.yml b/modules/cellranger/mkfastq/meta.yml → modules/nf-core/cellranger/mkfastq/meta.yml
diff --git a/modules/cellranger/mkgtf/main.nf → modules/nf-core/cellranger/mkgtf/main.nf b/modules/cellranger/mkgtf/main.nf → modules/nf-core/cellranger/mkgtf/main.nf
diff --git a/modules/cellranger/mkgtf/meta.yml → modules/nf-core/cellranger/mkgtf/meta.yml b/modules/cellranger/mkgtf/meta.yml → modules/nf-core/cellranger/mkgtf/meta.yml
diff --git a/modules/cellranger/mkref/main.nf → modules/nf-core/cellranger/mkref/main.nf b/modules/cellranger/mkref/main.nf → modules/nf-core/cellranger/mkref/main.nf
diff --git a/modules/cellranger/mkref/meta.yml → modules/nf-core/cellranger/mkref/meta.yml b/modules/cellranger/mkref/meta.yml → modules/nf-core/cellranger/mkref/meta.yml
diff --git a/modules/centrifuge/centrifuge/main.nf → ...les/nf-core/centrifuge/centrifuge/main.nf b/modules/centrifuge/centrifuge/main.nf → ...les/nf-core/centrifuge/centrifuge/main.nf
diff --git a/modules/centrifuge/centrifuge/meta.yml → ...es/nf-core/centrifuge/centrifuge/meta.yml b/modules/centrifuge/centrifuge/meta.yml → ...es/nf-core/centrifuge/centrifuge/meta.yml
diff --git a/modules/centrifuge/kreport/main.nf → modules/nf-core/centrifuge/kreport/main.nf b/modules/centrifuge/kreport/main.nf → modules/nf-core/centrifuge/kreport/main.nf
diff --git a/modules/centrifuge/kreport/meta.yml → modules/nf-core/centrifuge/kreport/meta.yml b/modules/centrifuge/kreport/meta.yml → modules/nf-core/centrifuge/kreport/meta.yml
diff --git a/modules/checkm/lineagewf/main.nf → modules/nf-core/checkm/lineagewf/main.nf b/modules/checkm/lineagewf/main.nf → modules/nf-core/checkm/lineagewf/main.nf
diff --git a/modules/checkm/lineagewf/meta.yml → modules/nf-core/checkm/lineagewf/meta.yml b/modules/checkm/lineagewf/meta.yml → modules/nf-core/checkm/lineagewf/meta.yml
diff --git a/modules/checkm/qa/main.nf → modules/nf-core/checkm/qa/main.nf b/modules/checkm/qa/main.nf → modules/nf-core/checkm/qa/main.nf
diff --git a/modules/checkm/qa/meta.yml → modules/nf-core/checkm/qa/meta.yml b/modules/checkm/qa/meta.yml → modules/nf-core/checkm/qa/meta.yml
diff --git a/modules/chromap/chromap/main.nf → modules/nf-core/chromap/chromap/main.nf b/modules/chromap/chromap/main.nf → modules/nf-core/chromap/chromap/main.nf
diff --git a/modules/chromap/chromap/meta.yml → modules/nf-core/chromap/chromap/meta.yml b/modules/chromap/chromap/meta.yml → modules/nf-core/chromap/chromap/meta.yml
diff --git a/modules/chromap/index/main.nf → modules/nf-core/chromap/index/main.nf b/modules/chromap/index/main.nf → modules/nf-core/chromap/index/main.nf
diff --git a/modules/chromap/index/meta.yml → modules/nf-core/chromap/index/meta.yml b/modules/chromap/index/meta.yml → modules/nf-core/chromap/index/meta.yml
diff --git a/modules/clonalframeml/main.nf → modules/nf-core/clonalframeml/main.nf b/modules/clonalframeml/main.nf → modules/nf-core/clonalframeml/main.nf
diff --git a/modules/clonalframeml/meta.yml → modules/nf-core/clonalframeml/meta.yml b/modules/clonalframeml/meta.yml → modules/nf-core/clonalframeml/meta.yml
diff --git a/modules/cmseq/polymut/main.nf → modules/nf-core/cmseq/polymut/main.nf b/modules/cmseq/polymut/main.nf → modules/nf-core/cmseq/polymut/main.nf
diff --git a/modules/cmseq/polymut/meta.yml → modules/nf-core/cmseq/polymut/meta.yml b/modules/cmseq/polymut/meta.yml → modules/nf-core/cmseq/polymut/meta.yml
diff --git a/modules/cnvkit/antitarget/main.nf → modules/nf-core/cnvkit/antitarget/main.nf b/modules/cnvkit/antitarget/main.nf → modules/nf-core/cnvkit/antitarget/main.nf
diff --git a/modules/cnvkit/antitarget/meta.yml → modules/nf-core/cnvkit/antitarget/meta.yml b/modules/cnvkit/antitarget/meta.yml → modules/nf-core/cnvkit/antitarget/meta.yml
diff --git a/modules/cnvkit/batch/main.nf → modules/nf-core/cnvkit/batch/main.nf b/modules/cnvkit/batch/main.nf → modules/nf-core/cnvkit/batch/main.nf
diff --git a/modules/cnvkit/batch/meta.yml → modules/nf-core/cnvkit/batch/meta.yml b/modules/cnvkit/batch/meta.yml → modules/nf-core/cnvkit/batch/meta.yml
diff --git a/modules/cnvkit/reference/main.nf → modules/nf-core/cnvkit/reference/main.nf b/modules/cnvkit/reference/main.nf → modules/nf-core/cnvkit/reference/main.nf
diff --git a/modules/cnvkit/reference/meta.yml → modules/nf-core/cnvkit/reference/meta.yml b/modules/cnvkit/reference/meta.yml → modules/nf-core/cnvkit/reference/meta.yml
diff --git a/modules/cnvpytor/callcnvs/main.nf → modules/nf-core/cnvpytor/callcnvs/main.nf b/modules/cnvpytor/callcnvs/main.nf → modules/nf-core/cnvpytor/callcnvs/main.nf
diff --git a/modules/cnvpytor/callcnvs/meta.yml → modules/nf-core/cnvpytor/callcnvs/meta.yml b/modules/cnvpytor/callcnvs/meta.yml → modules/nf-core/cnvpytor/callcnvs/meta.yml
diff --git a/modules/cnvpytor/histogram/main.nf → modules/nf-core/cnvpytor/histogram/main.nf b/modules/cnvpytor/histogram/main.nf → modules/nf-core/cnvpytor/histogram/main.nf
diff --git a/modules/cnvpytor/histogram/meta.yml → modules/nf-core/cnvpytor/histogram/meta.yml b/modules/cnvpytor/histogram/meta.yml → modules/nf-core/cnvpytor/histogram/meta.yml
diff --git a/modules/cnvpytor/importreaddepth/main.nf → .../nf-core/cnvpytor/importreaddepth/main.nf b/modules/cnvpytor/importreaddepth/main.nf → .../nf-core/cnvpytor/importreaddepth/main.nf
diff --git a/modules/cnvpytor/importreaddepth/meta.yml → ...nf-core/cnvpytor/importreaddepth/meta.yml b/modules/cnvpytor/importreaddepth/meta.yml → ...nf-core/cnvpytor/importreaddepth/meta.yml
diff --git a/modules/cnvpytor/partition/main.nf → modules/nf-core/cnvpytor/partition/main.nf b/modules/cnvpytor/partition/main.nf → modules/nf-core/cnvpytor/partition/main.nf
diff --git a/modules/cnvpytor/partition/meta.yml → modules/nf-core/cnvpytor/partition/meta.yml b/modules/cnvpytor/partition/meta.yml → modules/nf-core/cnvpytor/partition/meta.yml
diff --git a/modules/cnvpytor/view/main.nf → modules/nf-core/cnvpytor/view/main.nf b/modules/cnvpytor/view/main.nf → modules/nf-core/cnvpytor/view/main.nf
diff --git a/modules/cnvpytor/view/meta.yml → modules/nf-core/cnvpytor/view/meta.yml b/modules/cnvpytor/view/meta.yml → modules/nf-core/cnvpytor/view/meta.yml
diff --git a/...s/controlfreec/assesssignificance/main.nf → ...e/controlfreec/assesssignificance/main.nf b/...s/controlfreec/assesssignificance/main.nf → ...e/controlfreec/assesssignificance/main.nf
diff --git a/.../controlfreec/assesssignificance/meta.yml → .../controlfreec/assesssignificance/meta.yml b/.../controlfreec/assesssignificance/meta.yml → .../controlfreec/assesssignificance/meta.yml
diff --git a/modules/controlfreec/freec/main.nf → modules/nf-core/controlfreec/freec/main.nf b/modules/controlfreec/freec/main.nf → modules/nf-core/controlfreec/freec/main.nf
diff --git a/modules/controlfreec/freec/meta.yml → modules/nf-core/controlfreec/freec/meta.yml b/modules/controlfreec/freec/meta.yml → modules/nf-core/controlfreec/freec/meta.yml
diff --git a/modules/controlfreec/freec2bed/main.nf → ...es/nf-core/controlfreec/freec2bed/main.nf b/modules/controlfreec/freec2bed/main.nf → ...es/nf-core/controlfreec/freec2bed/main.nf
diff --git a/modules/controlfreec/freec2bed/meta.yml → ...s/nf-core/controlfreec/freec2bed/meta.yml b/modules/controlfreec/freec2bed/meta.yml → ...s/nf-core/controlfreec/freec2bed/meta.yml
diff --git a/modules/controlfreec/freec2circos/main.nf → ...nf-core/controlfreec/freec2circos/main.nf b/modules/controlfreec/freec2circos/main.nf → ...nf-core/controlfreec/freec2circos/main.nf
diff --git a/modules/controlfreec/freec2circos/meta.yml → ...f-core/controlfreec/freec2circos/meta.yml b/modules/controlfreec/freec2circos/meta.yml → ...f-core/controlfreec/freec2circos/meta.yml
diff --git a/modules/controlfreec/makegraph/main.nf → ...es/nf-core/controlfreec/makegraph/main.nf b/modules/controlfreec/makegraph/main.nf → ...es/nf-core/controlfreec/makegraph/main.nf
diff --git a/modules/controlfreec/makegraph/meta.yml → ...s/nf-core/controlfreec/makegraph/meta.yml b/modules/controlfreec/makegraph/meta.yml → ...s/nf-core/controlfreec/makegraph/meta.yml
diff --git a/modules/cooler/cload/main.nf → modules/nf-core/cooler/cload/main.nf b/modules/cooler/cload/main.nf → modules/nf-core/cooler/cload/main.nf
diff --git a/modules/cooler/cload/meta.yml → modules/nf-core/cooler/cload/meta.yml b/modules/cooler/cload/meta.yml → modules/nf-core/cooler/cload/meta.yml
diff --git a/modules/cooler/digest/main.nf → modules/nf-core/cooler/digest/main.nf b/modules/cooler/digest/main.nf → modules/nf-core/cooler/digest/main.nf
diff --git a/modules/cooler/digest/meta.yml → modules/nf-core/cooler/digest/meta.yml b/modules/cooler/digest/meta.yml → modules/nf-core/cooler/digest/meta.yml
diff --git a/modules/cooler/dump/main.nf → modules/nf-core/cooler/dump/main.nf b/modules/cooler/dump/main.nf → modules/nf-core/cooler/dump/main.nf
diff --git a/modules/cooler/dump/meta.yml → modules/nf-core/cooler/dump/meta.yml b/modules/cooler/dump/meta.yml → modules/nf-core/cooler/dump/meta.yml
diff --git a/modules/cooler/merge/main.nf → modules/nf-core/cooler/merge/main.nf b/modules/cooler/merge/main.nf → modules/nf-core/cooler/merge/main.nf
diff --git a/modules/cooler/merge/meta.yml → modules/nf-core/cooler/merge/meta.yml b/modules/cooler/merge/meta.yml → modules/nf-core/cooler/merge/meta.yml
diff --git a/modules/cooler/zoomify/main.nf → modules/nf-core/cooler/zoomify/main.nf b/modules/cooler/zoomify/main.nf → modules/nf-core/cooler/zoomify/main.nf
diff --git a/modules/cooler/zoomify/meta.yml → modules/nf-core/cooler/zoomify/meta.yml b/modules/cooler/zoomify/meta.yml → modules/nf-core/cooler/zoomify/meta.yml
diff --git a/modules/csvtk/concat/main.nf → modules/nf-core/csvtk/concat/main.nf b/modules/csvtk/concat/main.nf → modules/nf-core/csvtk/concat/main.nf
diff --git a/modules/csvtk/concat/meta.yml → modules/nf-core/csvtk/concat/meta.yml b/modules/csvtk/concat/meta.yml → modules/nf-core/csvtk/concat/meta.yml
diff --git a/modules/csvtk/split/main.nf → modules/nf-core/csvtk/split/main.nf b/modules/csvtk/split/main.nf → modules/nf-core/csvtk/split/main.nf