Restructure nf-core/modules repo (nf-core#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 <edmund.a.miller@protonmail.com>
matthdsm · Oct 5, 2022 · 5621f00 · 5621f00
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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
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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
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diff --git a/modules/bclconvert/LICENSE → modules/nf-core/bclconvert/LICENSE b/modules/bclconvert/LICENSE → modules/nf-core/bclconvert/LICENSE
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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
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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
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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
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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
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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
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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
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diff --git a/modules/biobambam/bammarkduplicates2/main.nf → ...core/biobambam/bammarkduplicates2/main.nf b/modules/biobambam/bammarkduplicates2/main.nf → ...core/biobambam/bammarkduplicates2/main.nf
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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diff --git a/...les/bracken/combinebrackenoutputs/main.nf → ...ore/bracken/combinebrackenoutputs/main.nf b/...les/bracken/combinebrackenoutputs/main.nf → ...ore/bracken/combinebrackenoutputs/main.nf
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diff --git a/modules/busco/main.nf → modules/nf-core/busco/main.nf b/modules/busco/main.nf → modules/nf-core/busco/main.nf
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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