├── .editorconfig ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── ... │ ├── branch.yml │ ├── docker.yml │ └── docs.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── .prettierignore ├── .prettierrc.yml ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── assets ├── email_template.html ├── email_template.txt ├── multiqc_config.yml ├── nf-core-viroprofiler_logo_light.png ├── samplesheet.csv ├── samplesheet_contigs.csv ├── samplesheet_testfull.csv ├── schema_input.json └── sendmail_template.txt ├── bin ├── anicalc.py ├── aniclust.py ├── calc_qvalue.r ├── combine_taxa.py ├── concat_vrhyme_bin.py ├── correct_spades_contig_length.py ├── create_contamref_idx.sh ├── create_dram_config.py ├── create_tse.r ├── extract_gene_by_contig_id.py ├── gene_to_genome.py ├── mask_genome.sh ├── parse_NRCLib_clusters.py ├── parse_eggnog.py ├── parse_mmseqsTaxa.py ├── parse_vContact2_vc.py ├── pretty_gff.py └── run_checkv.sh ├── conf ├── base.config ├── igenomes.config ├── modules.config └── test.config ├── custom.config ├── docker ├── viroprofiler-abundance │ ├── Dockerfile │ └── env_abundance.yml ├── viroprofiler-base │ ├── Dockerfile │ ├── env_base.yml │ ├── env_checkv.yml │ └── env_virsorter2.yml ├── viroprofiler-binning │ ├── Dockerfile │ ├── env_binning.yml │ ├── env_dvf.yml │ └── env_vrhyme.yml ├── viroprofiler-bracken │ ├── Dockerfile │ ├── env_bracken.yml │ └── rsync_from_ncbi.pl ├── viroprofiler-geneannot │ ├── Dockerfile │ ├── database_handler.py │ ├── database_handler_bak.py │ ├── env_abricate.yml │ ├── env_dram.yml │ └── env_emapper.yml ├── viroprofiler-host │ ├── Dockerfile │ ├── activate │ │ └── update_bioperl.sh │ ├── deactivate │ │ └── update_bioperl.sh │ └── env_host.yml ├── viroprofiler-phamb │ ├── Dockerfile │ └── env_phamb.yml ├── viroprofiler-replicyc │ ├── Dockerfile │ ├── env_bacphlip.yml │ └── env_replidec.yml ├── viroprofiler-taxa │ ├── Dockerfile │ └── env_taxa.yml ├── viroprofiler-vibrant │ ├── Dockerfile │ └── env_vibrant.yml └── viroprofiler-virsorter2 │ ├── Dockerfile │ └── env_virsorter2.yml ├── docs ├── .requirements.txt ├── README.md ├── config.md ├── images │ ├── lablogo.png │ ├── mqc_fastqc_adapter.png │ ├── mqc_fastqc_counts.png │ ├── mqc_fastqc_quality.png │ └── viroprofiler.png ├── index.md ├── installation.md ├── output.md ├── profiles.md ├── quickstart.md ├── tutorial.md └── usage.md ├── lib ├── NfcoreSchema.groovy ├── NfcoreTemplate.groovy ├── Utils.groovy ├── WorkflowMain.groovy ├── WorkflowViroprofiler.groovy └── nfcore_external_java_deps.jar ├── main.nf ├── mkdocs.yml ├── modules.json ├── modules ├── local │ ├── abricate.nf │ ├── abundance.nf │ ├── annotation.nf │ ├── base.nf │ ├── binning.nf │ ├── bracken.nf │ ├── contig_library.nf │ ├── decontam.nf │ ├── gene_library.nf │ ├── replicyc.nf │ ├── setup_db.nf │ 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