renaming NF_MGIllumina to NF_MGIllumina-A

nasa · Oct 23, 2024 · cfdd9a7 · cfdd9a7
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diff --git a/..._Documentation/NF_MGIllumina/CHANGELOG.md → ...ocumentation/NF_MGIllumina-A/CHANGELOG.md b/..._Documentation/NF_MGIllumina/CHANGELOG.md → ...ocumentation/NF_MGIllumina-A/CHANGELOG.md
diff --git a/...low_Documentation/NF_MGIllumina/README.md → ...w_Documentation/NF_MGIllumina-A/README.md b/...low_Documentation/NF_MGIllumina/README.md → ...w_Documentation/NF_MGIllumina-A/README.md
diff --git a/...n/NF_MGIllumina/workflow_code/PE_file.csv → ...NF_MGIllumina-A/workflow_code/PE_file.csv b/...n/NF_MGIllumina/workflow_code/PE_file.csv → ...NF_MGIllumina-A/workflow_code/PE_file.csv
diff --git a/...n/NF_MGIllumina/workflow_code/SE_file.csv → ...NF_MGIllumina-A/workflow_code/SE_file.csv b/...n/NF_MGIllumina/workflow_code/SE_file.csv → ...NF_MGIllumina-A/workflow_code/SE_file.csv
diff --git a/...-gen-metagenomics-file-associations-table → ...-gen-metagenomics-file-associations-table b/...-gen-metagenomics-file-associations-table → ...-gen-metagenomics-file-associations-table
diff --git a/.../bin/GL-gen-processed-metagenomics-readme → .../bin/GL-gen-processed-metagenomics-readme b/.../bin/GL-gen-processed-metagenomics-readme → .../bin/GL-gen-processed-metagenomics-readme
diff --git a/...n/GL-validate-processed-metagenomics-data → ...n/GL-validate-processed-metagenomics-data b/...n/GL-validate-processed-metagenomics-data → ...n/GL-validate-processed-metagenomics-data
diff --git a/...Illumina/workflow_code/bin/clean-paths.sh → ...lumina-A/workflow_code/bin/clean-paths.sh b/...Illumina/workflow_code/bin/clean-paths.sh → ...lumina-A/workflow_code/bin/clean-paths.sh
diff --git a/...kflow_code/bin/combine-all-gene-tables.py → ...kflow_code/bin/combine-all-gene-tables.py b/...kflow_code/bin/combine-all-gene-tables.py → ...kflow_code/bin/combine-all-gene-tables.py
diff --git a/...vel-coverages-annots-and-tax-per-group.py → ...vel-coverages-annots-and-tax-per-group.py b/...vel-coverages-annots-and-tax-per-group.py → ...vel-coverages-annots-and-tax-per-group.py
diff --git a/...mina/workflow_code/bin/create_runsheet.sh → ...na-A/workflow_code/bin/create_runsheet.sh b/...mina/workflow_code/bin/create_runsheet.sh → ...na-A/workflow_code/bin/create_runsheet.sh
diff --git a/...a/workflow_code/bin/download-GTDBTK-db.sh → ...A/workflow_code/bin/download-GTDBTK-db.sh b/...a/workflow_code/bin/download-GTDBTK-db.sh → ...A/workflow_code/bin/download-GTDBTK-db.sh
diff --git a/.../bin/format-contig-tax-classifications.sh → .../bin/format-contig-tax-classifications.sh b/.../bin/format-contig-tax-classifications.sh → .../bin/format-contig-tax-classifications.sh
diff --git a/...de/bin/format-gene-tax-classifications.sh → ...de/bin/format-gene-tax-classifications.sh b/...de/bin/format-gene-tax-classifications.sh → ...de/bin/format-gene-tax-classifications.sh
diff --git a/...generate-assembly-based-overview-table.sh → ...generate-assembly-based-overview-table.sh b/...generate-assembly-based-overview-table.sh → ...generate-assembly-based-overview-table.sh
diff --git a/...na/workflow_code/bin/get-cov-and-depth.sh → ...-A/workflow_code/bin/get-cov-and-depth.sh b/...na/workflow_code/bin/get-cov-and-depth.sh → ...-A/workflow_code/bin/get-cov-and-depth.sh
diff --git a/...de/bin/get_MAGs_estimates_and_taxonomy.sh → ...de/bin/get_MAGs_estimates_and_taxonomy.sh b/...de/bin/get_MAGs_estimates_and_taxonomy.sh → ...de/bin/get_MAGs_estimates_and_taxonomy.sh
diff --git a/...ina/workflow_code/bin/parse-MAG-annots.py → ...a-A/workflow_code/bin/parse-MAG-annots.py b/...ina/workflow_code/bin/parse-MAG-annots.py → ...a-A/workflow_code/bin/parse-MAG-annots.py
diff --git a/.../workflow_code/bin/prepull_singularity.sh → .../workflow_code/bin/prepull_singularity.sh b/.../workflow_code/bin/prepull_singularity.sh → .../workflow_code/bin/prepull_singularity.sh
diff --git a/...llumina/workflow_code/bin/swap-MAG-IDs.py → ...umina-A/workflow_code/bin/swap-MAG-IDs.py b/...llumina/workflow_code/bin/swap-MAG-IDs.py → ...umina-A/workflow_code/bin/swap-MAG-IDs.py
diff --git a/.../workflow_code/config/bbtools_adapters.fa → .../workflow_code/config/bbtools_adapters.fa b/.../workflow_code/config/bbtools_adapters.fa → .../workflow_code/config/bbtools_adapters.fa
diff --git a/...umina/workflow_code/config/multiqc.config → ...ina-A/workflow_code/config/multiqc.config b/...umina/workflow_code/config/multiqc.config → ...ina-A/workflow_code/config/multiqc.config
diff --git a/...NF_MGIllumina/workflow_code/envs/bit.yaml → ..._MGIllumina-A/workflow_code/envs/bit.yaml b/...NF_MGIllumina/workflow_code/envs/bit.yaml → ..._MGIllumina-A/workflow_code/envs/bit.yaml
diff --git a/...NF_MGIllumina/workflow_code/envs/cat.yaml → ..._MGIllumina-A/workflow_code/envs/cat.yaml b/...NF_MGIllumina/workflow_code/envs/cat.yaml → ..._MGIllumina-A/workflow_code/envs/cat.yaml
diff --git a/...MGIllumina/workflow_code/envs/checkm.yaml → ...Illumina-A/workflow_code/envs/checkm.yaml b/...MGIllumina/workflow_code/envs/checkm.yaml → ...Illumina-A/workflow_code/envs/checkm.yaml
diff --git a/...GIllumina/workflow_code/envs/genelab.yaml → ...llumina-A/workflow_code/envs/genelab.yaml b/...GIllumina/workflow_code/envs/genelab.yaml → ...llumina-A/workflow_code/envs/genelab.yaml
diff --git a/...GIllumina/workflow_code/envs/gtdb-tk.yaml → ...llumina-A/workflow_code/envs/gtdb-tk.yaml b/...GIllumina/workflow_code/envs/gtdb-tk.yaml → ...llumina-A/workflow_code/envs/gtdb-tk.yaml
diff --git a/...GIllumina/workflow_code/envs/humann3.yaml → ...llumina-A/workflow_code/envs/humann3.yaml b/...GIllumina/workflow_code/envs/humann3.yaml → ...llumina-A/workflow_code/envs/humann3.yaml
diff --git a/...Illumina/workflow_code/envs/image_def.bit → ...lumina-A/workflow_code/envs/image_def.bit b/...Illumina/workflow_code/envs/image_def.bit → ...lumina-A/workflow_code/envs/image_def.bit
diff --git a/...mina/workflow_code/envs/image_def.genelab → ...na-A/workflow_code/envs/image_def.genelab b/...mina/workflow_code/envs/image_def.genelab → ...na-A/workflow_code/envs/image_def.genelab
diff --git a/...umina/workflow_code/envs/keggdecoder.yaml → ...ina-A/workflow_code/envs/keggdecoder.yaml b/...umina/workflow_code/envs/keggdecoder.yaml → ...ina-A/workflow_code/envs/keggdecoder.yaml
diff --git a/...llumina/workflow_code/envs/kofamscan.yaml → ...umina-A/workflow_code/envs/kofamscan.yaml b/...llumina/workflow_code/envs/kofamscan.yaml → ...umina-A/workflow_code/envs/kofamscan.yaml
diff --git a/...GIllumina/workflow_code/envs/mapping.yaml → ...llumina-A/workflow_code/envs/mapping.yaml b/...GIllumina/workflow_code/envs/mapping.yaml → ...llumina-A/workflow_code/envs/mapping.yaml
diff --git a/...GIllumina/workflow_code/envs/megahit.yaml → ...llumina-A/workflow_code/envs/megahit.yaml b/...GIllumina/workflow_code/envs/megahit.yaml → ...llumina-A/workflow_code/envs/megahit.yaml
diff --git a/...GIllumina/workflow_code/envs/metabat.yaml → ...llumina-A/workflow_code/envs/metabat.yaml b/...GIllumina/workflow_code/envs/metabat.yaml → ...llumina-A/workflow_code/envs/metabat.yaml
diff --git a/...Illumina/workflow_code/envs/prodigal.yaml → ...lumina-A/workflow_code/envs/prodigal.yaml b/...Illumina/workflow_code/envs/prodigal.yaml → ...lumina-A/workflow_code/envs/prodigal.yaml
diff --git a/.../NF_MGIllumina/workflow_code/envs/qc.yaml → ...F_MGIllumina-A/workflow_code/envs/qc.yaml b/.../NF_MGIllumina/workflow_code/envs/qc.yaml → ...F_MGIllumina-A/workflow_code/envs/qc.yaml
diff --git a/...ation/NF_MGIllumina/workflow_code/main.nf → ...ion/NF_MGIllumina-A/workflow_code/main.nf b/...ation/NF_MGIllumina/workflow_code/main.nf → ...ion/NF_MGIllumina-A/workflow_code/main.nf
diff --git a/...llumina/workflow_code/modules/assembly.nf → ...umina-A/workflow_code/modules/assembly.nf b/...llumina/workflow_code/modules/assembly.nf → ...umina-A/workflow_code/modules/assembly.nf
diff --git a/...kflow_code/modules/assembly_annotation.nf → ...kflow_code/modules/assembly_annotation.nf b/...kflow_code/modules/assembly_annotation.nf → ...kflow_code/modules/assembly_annotation.nf
diff --git a/...code/modules/assembly_based_processing.nf → ...code/modules/assembly_based_processing.nf b/...code/modules/assembly_based_processing.nf → ...code/modules/assembly_based_processing.nf
diff --git a/...Illumina/workflow_code/modules/binning.nf → ...lumina-A/workflow_code/modules/binning.nf b/...Illumina/workflow_code/modules/binning.nf → ...lumina-A/workflow_code/modules/binning.nf
diff --git a/...code/modules/combine_contig_annotation.nf → ...code/modules/combine_contig_annotation.nf b/...code/modules/combine_contig_annotation.nf → ...code/modules/combine_contig_annotation.nf
diff --git a/...llumina/workflow_code/modules/coverage.nf → ...umina-A/workflow_code/modules/coverage.nf b/...llumina/workflow_code/modules/coverage.nf → ...umina-A/workflow_code/modules/coverage.nf
diff --git a/.../workflow_code/modules/create_runsheet.nf → .../workflow_code/modules/create_runsheet.nf b/.../workflow_code/modules/create_runsheet.nf → .../workflow_code/modules/create_runsheet.nf
diff --git a/...orkflow_code/modules/database_creation.nf → ...orkflow_code/modules/database_creation.nf b/...orkflow_code/modules/database_creation.nf → ...orkflow_code/modules/database_creation.nf
diff --git a/...Illumina/workflow_code/modules/genelab.nf → ...lumina-A/workflow_code/modules/genelab.nf b/...Illumina/workflow_code/modules/genelab.nf → ...lumina-A/workflow_code/modules/genelab.nf
diff --git a/...rkflow_code/modules/quality_assessment.nf → ...rkflow_code/modules/quality_assessment.nf b/...rkflow_code/modules/quality_assessment.nf → ...rkflow_code/modules/quality_assessment.nf
diff --git a/...low_code/modules/read_based_processing.nf → ...low_code/modules/read_based_processing.nf b/...low_code/modules/read_based_processing.nf → ...low_code/modules/read_based_processing.nf
diff --git a/...ina/workflow_code/modules/read_mapping.nf → ...a-A/workflow_code/modules/read_mapping.nf b/...ina/workflow_code/modules/read_mapping.nf → ...a-A/workflow_code/modules/read_mapping.nf
diff --git a/...na/workflow_code/modules/summarize_MAG.nf → ...-A/workflow_code/modules/summarize_MAG.nf b/...na/workflow_code/modules/summarize_MAG.nf → ...-A/workflow_code/modules/summarize_MAG.nf
diff --git a/...es/summarize_assembly-based_processing.nf → ...es/summarize_assembly-based_processing.nf b/...es/summarize_assembly-based_processing.nf → ...es/summarize_assembly-based_processing.nf
diff --git a/...a/workflow_code/modules/summarize_bins.nf → ...A/workflow_code/modules/summarize_bins.nf b/...a/workflow_code/modules/summarize_bins.nf → ...A/workflow_code/modules/summarize_bins.nf
diff --git a/...lumina/workflow_code/modules/zip_fasta.nf → ...mina-A/workflow_code/modules/zip_fasta.nf b/...lumina/workflow_code/modules/zip_fasta.nf → ...mina-A/workflow_code/modules/zip_fasta.nf
diff --git a/..._MGIllumina/workflow_code/nextflow.config → ...GIllumina-A/workflow_code/nextflow.config b/..._MGIllumina/workflow_code/nextflow.config → ...GIllumina-A/workflow_code/nextflow.config
diff --git a/...mina/workflow_code/post_processing.config → ...na-A/workflow_code/post_processing.config b/...mina/workflow_code/post_processing.config → ...na-A/workflow_code/post_processing.config
diff --git a/...Illumina/workflow_code/post_processing.nf → ...lumina-A/workflow_code/post_processing.nf b/...Illumina/workflow_code/post_processing.nf → ...lumina-A/workflow_code/post_processing.nf
diff --git a/...Illumina/workflow_code/slurm_submit.slurm → ...lumina-A/workflow_code/slurm_submit.slurm b/...Illumina/workflow_code/slurm_submit.slurm → ...lumina-A/workflow_code/slurm_submit.slurm