├── .github └── workflows │ ├── latest-dry-run.yaml │ ├── latest-fast.yaml │ ├── latest-full.yaml │ ├── stable-apptainer_A.yaml │ ├── stable-apptainer_B.yaml │ └── stable-conda.yaml ├── .gitignore ├── .readthedocs.yaml ├── CONTRIBUTORS.md ├── Dockerfile ├── LICENSE ├── README.md ├── changelog.txt ├── citation.cff ├── comparem2 ├── comparem2.Rproj ├── config └── config.yaml ├── docs ├── 05 quick start.md ├── 10 installation.md ├── 20 usage.md ├── 30 what analyses does it do.md ├── 80 future functionality.md ├── 82 contributors.md ├── 99 citation.md ├── help_text.txt ├── index.md ├── practical examples.md ├── requirements.in └── requirements.txt ├── dynamic_report ├── README.md └── workflow │ ├── Snakefile │ ├── envs │ └── r-markdown.yaml │ └── scripts │ ├── _report_end_script.sh │ ├── ape_plot.pdf │ ├── report_template.rmd │ ├── section_amrfinder.rmd │ ├── section_assembly_stats.rmd │ ├── section_bakta.rmd │ ├── section_checkm2.rmd │ ├── section_dbcan.rmd │ ├── section_eggnog.rmd │ ├── section_eggnog_cazy.rmd │ ├── section_gapseq_find.rmd │ ├── section_gtdbtk.rmd │ ├── section_kegg_pathway.rmd │ ├── section_mashtree.rmd │ ├── section_mlst.rmd │ ├── section_panaroo.rmd │ ├── section_prokka.rmd │ ├── section_sequence_lengths.rmd │ └── section_snp_dists.rmd ├── environment.yaml ├── mkdocs.yml ├── profile ├── README.md ├── apptainer │ ├── concrete-integration │ │ ├── pbs-qut-lyra │ │ │ └── config.yaml │ │ ├── slurm-au-genomedk │ │ │ └── config.yaml │ │ ├── slurm-nmbu-orion │ │ │ └── config.yaml │ │ └── slurm-sigma2-saga │ │ │ └── config.yaml │ ├── default │ │ └── config.yaml │ ├── template-pbs │ │ └── config.yaml │ └── template-slurm │ │ └── config.yaml └── conda │ ├── concrete-integration │ ├── pbs-qut-lyra │ │ └── config.yaml │ ├── slurm-au-genomedk │ │ └── config.yaml │ ├── slurm-nmbu-orion │ │ └── config.yaml │ └── slurm-sigma2-saga │ │ └── config.yaml │ ├── default │ └── config.yaml │ ├── template-pbs │ └── config.yaml │ └── template-slurm │ └── config.yaml ├── readme-development.md ├── resources ├── README.md ├── ass.txt ├── enable_passthrough_parameters.sh ├── env_current.yaml ├── env_stable.yaml ├── footer.md ├── ko00001.json └── logo.txt ├── tests ├── E._faecium │ ├── fna.zip │ └── report_E._faecium.html.zip ├── E._faecium_plasmids │ └── fna.zip ├── MAGs │ └── fna.zip ├── Methanoflorens │ ├── fna.zip │ └── report_Methanoflorens.html.zip ├── README.md └── strachan_campylo │ ├── fna.zip │ └── report_strachan_campylo.html.zip └── workflow ├── Snakefile ├── envs ├── README.md ├── amrfinder.yaml ├── antismash.yaml ├── any2fasta.yaml ├── assembly-stats.yaml ├── bakta.yaml ├── carveme.yaml ├── checkm2.yaml ├── dbcan.yaml ├── diamond.yaml ├── eggnog.yaml ├── fasttree.yaml ├── gapseq.yaml ├── gtdbtk.yaml ├── interproscan.yaml ├── iqtree.yaml ├── mashtree.yaml ├── mlst.yaml ├── ncbi_datasets.yaml ├── panaroo.yaml ├── prokka.yaml ├── r-clusterProfiler.yaml ├── seqkit.yaml ├── snp-dists.yaml ├── treecluster.yaml └── wget.yaml ├── rules ├── 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