├── .github └── workflows │ └── pipeline.yaml ├── .gitignore ├── DO_NOT_BACKUP_THIS_FOLDER ├── LICENSE ├── README.md ├── Snakefile ├── benchmark ├── 01_Standard-Kraken-Bracken-DBs.ipynb ├── 02_CAMI-QC.ipynb ├── 03_CAMI_profiles.ipynb ├── 04_CAMI_stats.ipynb ├── 05_BGI_profiles.ipynb └── 06_BGI_stats.ipynb ├── bin ├── Snakefile ├── bracken │ └── Snakefile ├── dirs ├── envs │ ├── humann2.yaml │ └── kraken2.yaml ├── humann2 │ └── Snakefile ├── kraken2 │ └── Snakefile └── scripts │ ├── annotate_genes.py │ ├── bracken-build.py │ ├── download_taxonomy.sh │ ├── filter_seqs.py │ ├── kraken2-build │ ├── kraken2_rename_genome.py │ └── log_summarize.py ├── config.yaml ├── images └── struo_workflow.png ├── notebooks ├── .ipynb_checkpoints │ └── 01_GTDB_metadata_summary-checkpoint.ipynb ├── release86 │ ├── 01_GTDB_metadata_summary.ipynb │ └── 02_LLMGP-DB_resources.ipynb └── release89 │ ├── 01_GTDB_metadata_summary.ipynb │ └── 02_LLMGP-DB_resources.ipynb ├── snakemake_clean.sh ├── snakemake_conda-list.sh ├── snakemake_sge.sh ├── tests ├── accession.txt ├── config_default.yaml ├── data │ ├── clusters_rep-seqs.faa.gz │ ├── clusters_rep-seqs.fna.gz │ └── genomes │ │ ├── GCA_000214495.2_ASM21449v1_genomic.fna.gz │ │ ├── GCA_000221545.2_ASM22154v1_genomic.fna.gz │ │ ├── GCA_000764165.1_ASM76416v1_genomic.fna.gz │ │ ├── GCA_002009845.1_ASM200984v1_genomic.fna.gz │ │ └── GCA_900143645.1_IMG-taxon_2582580727_annotated_assembly_genomic.fna.gz ├── metadata_n3.tsv └── samples │ ├── samples_n10.txt │ ├── samples_n100.txt │ ├── samples_n3.txt │ └── samples_n5.txt ├── tutorial ├── 01_Example_Struo_Run.ipynb └── struo_env.yaml └── util_scripts ├── GTDB_metadata_filter.R ├── genome_download.R └── tree_prune.py /.github/workflows/pipeline.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/leylabmpi/Struo/HEAD/.github/workflows/pipeline.yaml 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