├── .gitattributes ├── .github ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md ├── markdownlint.yml └── workflows │ ├── branch.yml │ ├── ci.yml │ └── linting.yml ├── .gitignore ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── assets ├── email_template.html ├── email_template.txt ├── multiqc_config.yaml ├── nf-core-nanoclust_logo.png └── sendmail_template.txt ├── bin ├── kmer_freq.py ├── markdown_to_html.py ├── markdown_to_html.r └── scrape_software_versions.py ├── conda_envs ├── cluster_plot_pool │ ├── Dockerfile │ └── environment.yml ├── consensus_classification │ ├── Dockerfile │ └── environment.yml ├── demultiplex │ ├── Dockerfile │ └── environment.yml ├── demultiplex_porechop │ ├── Dockerfile │ └── environment.yml ├── draft_selection │ ├── Dockerfile │ └── environment.yml ├── fastqc │ ├── Dockerfile │ └── environment.yml ├── kmer_freqs │ ├── Dockerfile │ └── environment.yml ├── medaka_pass │ ├── Dockerfile │ └── environment.yml ├── output_documentation │ ├── Dockerfile │ └── environment.yml ├── qc_fastp │ ├── Dockerfile │ └── environment.yml ├── racon_pass │ ├── Dockerfile │ └── environment.yml ├── read_clustering │ ├── Dockerfile │ └── environment.yml ├── read_correction │ ├── Dockerfile │ └── environment.yml └── split_by_cluster │ ├── Dockerfile │ └── environment.yml ├── conf ├── 18S.conf ├── awsbatch.config ├── base.config ├── igenomes.config └── test.config ├── docs ├── 2usage.md ├── 3pipeline_output.md ├── README.md ├── images │ └── nf-core-nanoclust_logo.png └── index.md ├── main.nf ├── mkdocs.yml ├── nextflow.config ├── templates ├── .ipynb_checkpoints │ └── umap_hdbscan-checkpoint.py ├── fastani_ranking.py ├── get_abundance.py ├── kmer_freq.py ├── plot_abundances_pool.py ├── umap_hdbscan.py └── umap_plot.py └── test_datasets └── mock4_run3bc08_5000.fastq /.gitattributes: -------------------------------------------------------------------------------- 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