├── .github └── workflows │ └── run_pipeline.yml ├── .gitignore ├── ARGprofiler_pipeline.png ├── LICENSE ├── README.md ├── Snakefile ├── config └── config.yaml ├── env └── environment_argprofiler.yaml ├── input.json ├── prerequisites ├── ARGextender │ └── targetAsm.pl ├── db_motus │ └── README.md ├── db_panres │ └── README.md └── mapstat_filtering │ ├── exclusion_seqs.tsv │ ├── mapstatFilters.R │ ├── pan.fa │ ├── pan.zip │ ├── panRes_gene_filtering.nb.html │ └── pan_master_gene_tbl.tsv ├── profile_argprofiler ├── cluster_computerome.json └── config.yaml └── rules ├── analysis_paired_read.smk ├── analysis_single_read.smk └── fetch_db.smk /.github/workflows/run_pipeline.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/genomicepidemiology/ARGprofiler/HEAD/.github/workflows/run_pipeline.yml -------------------------------------------------------------------------------- /.gitignore: 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