├── .github ├── ISSUE_TEMPLATE │ └── bug_report.md └── workflows │ └── main.yml ├── .gitignore ├── CITATION.cff ├── LICENSE ├── README.md ├── cicd ├── Dockerfile ├── Dockerfile_CI ├── base_environment.yml ├── build.sh ├── install.bash └── meta.yaml ├── config ├── mgmp_config.json └── mgmt_config.json ├── resources ├── default_config.json ├── minimum_envs │ ├── .README │ ├── assembly_min.yaml │ ├── binning_min.yaml │ ├── de_analysis_min.yaml │ ├── gene_calling_min.yaml │ ├── keggcharter_min.yaml │ ├── merge_reads_min.yaml │ ├── metaproteomics_min.yaml │ ├── normalization_min.yaml │ ├── preprocess_min.yaml │ ├── quantification_min.yaml │ ├── recognizer_min.yaml │ ├── reports_min.yaml │ ├── seqkit_min.yaml │ ├── summary_min.yaml │ └── upimapi_min.yaml ├── mosca_logo.png ├── mosca_logo.txt └── wiki │ ├── .README │ ├── community-grey.png │ ├── community-icon.svg │ ├── dashboard-grey.png │ ├── dashboard-icon.svg │ ├── gear-grey.png │ ├── gear-icon.svg │ ├── mosca-grey.png │ ├── parts-icon.svg │ ├── technical-icon.svg │ ├── unpacking-grey.png │ └── unpacking-icon.svg └── workflow ├── Snakefile ├── envs ├── assembly.yaml ├── binning.yaml ├── de_analysis.yaml ├── gene_calling.yaml ├── keggcharter.yaml ├── merge_reads.yaml ├── metaproteomics.yaml ├── normalization.yaml ├── preprocess.yaml ├── quantification.yaml ├── recognizer.yaml ├── reports.yaml ├── seqkit.yaml ├── summary.yaml └── upimapi.yaml ├── mosca.py ├── rules ├── assembly.smk ├── binning.smk ├── common.smk ├── de_analysis.smk ├── entry_report.smk ├── gene_calling.smk ├── general_report.smk ├── keggcharter.smk ├── metaproteomics.smk ├── normalization.smk ├── preprocess.smk ├── quantification.smk ├── recognizer.smk ├── summary_report.smk └── upimapi.smk ├── schemas └── config.schema.yaml └── scripts ├── assembly.py ├── binning.py ├── common └── __init__.py ├── de_analysis.R ├── entry_report.py ├── general_report.py ├── metaproteomics.py ├── mosca_tools.py ├── normalization.R ├── preprocess.py ├── 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