{
    "fasta_txt": "",
    "workflow_name": "metagenomics",
    "anvi_gen_contigs_database": {
        "--project-name": "{group}",
        "--description": "",
        "--skip-gene-calling": "",
        "--external-gene-calls": "",
        "--ignore-internal-stop-codons": "",
        "--skip-mindful-splitting": "",
        "--contigs-fasta": "",
        "--split-length": "",
        "--kmer-size": "",
        "--prodigal-translation-table": "",
        "threads": ""
    },
    "centrifuge": {
        "threads": 12,
        "run": true,
        "db": "/pool/genomics/stri_istmobiome/dbs/centrifuge_dbs/p+h+v"
    },
    "anvi_run_hmms": {
        "run": true,
        "threads": 5,
        "--installed-hmm-profile": "",
        "--hmm-profile-dir": ""
    },
    "anvi_run_ncbi_cogs": {
        "run": true,
        "threads": 5,
        "--cog-data-dir": "/pool/genomics/stri_istmobiome/dbs/cog_db/",
        "--sensitive": "",
        "--temporary-dir-path": "/pool/genomics/stri_istmobiome/dbs/cog_db/tmp/",
        "--search-with": ""
    },
    "anvi_run_scg_taxonomy": {
        "run": true,
        "threads": 6,
        "--scgs-taxonomy-data-dir": "/pool/genomics/stri_istmobiome/dbs/scgs-taxonomy-data/"
    },
    "anvi_script_reformat_fasta": {
        "run": true,
        "--prefix": "{group}",
        "--simplify-names": true,
        "--keep-ids": "",
        "--exclude-ids": "",
        "--min-len": "1000",
        "threads": ""
    },
    "emapper": {
        "--database": "bact",
        "--usemem": true,
        "--override": true,
        "path_to_emapper_dir": "",
        "threads": ""
    },
    "anvi_script_run_eggnog_mapper": {
        "--use-version": "0.12.6",
        "run": "",
        "--cog-data-dir": "/pool/genomics/stri_istmobiome/dbs/cog_db/",
        "--drop-previous-annotations": "",
        "threads": 20
    },
    "samples_txt": "samples.txt",
    "metaspades": {
        "additional_params": "--only-assembler",
        "threads": 7,
        "run": "",
        "use_scaffolds": ""
    },
    "megahit": {
        "--min-contig-len": 1000,
        "--memory": 0.8,
        "threads": 20,
        "run": true,
        "--min-count": "",
        "--k-min": "",
        "--k-max": "",
        "--k-step": "",
        "--k-list": "",
        "--no-mercy": "",
        "--no-bubble": "",
        "--merge-level": "",
        "--prune-level": "",
        "--prune-depth": "",
        "--low-local-ratio": "",
        "--max-tip-len": "",
        "--no-local": "",
        "--kmin-1pass": "",
        "--presets": "meta-sensitive",
        "--mem-flag": "",
        "--use-gpu": "",
        "--gpu-mem": "",
        "--keep-tmp-files": "",
        "--tmp-dir": "",
        "--continue": true,
        "--verbose": ""
    },
    "idba_ud": {
        "--min_contig": 1000,
        "threads": 7,
        "run": "",
        "--mink": "",
        "--maxk": "",
        "--step": "",
        "--inner_mink": "",
        "--inner_step": "",
        "--prefix": "",
        "--min_count": "",
        "--min_support": "",
        "--seed_kmer": "",
        "--similar": "",
        "--max_mismatch": "",
        "--min_pairs": "",
        "--no_bubble": "",
        "--no_local": "",
        "--no_coverage": "",
        "--no_correct": "",
        "--pre_correction": ""
    },
    "iu_filter_quality_minoche": {
        "run": true,
        "--ignore-deflines": true,
        "--visualize-quality-curves": "",
        "--limit-num-pairs": "",
        "--print-qual-scores": "",
        "--store-read-fate": "",
        "threads": ""
    },
    "gzip_fastqs": {
        "run": true,
        "threads": ""
    },
    "bowtie": {
        "additional_params": "--no-unal",
        "threads": 3
    },
    "samtools_view": {
        "additional_params": "-F 4",
        "threads": ""
    },
    "anvi_profile": {
        "threads": 5,
        "--sample-name": "{sample}",
        "--overwrite-output-destinations": true,
        "--report-variability-full": "",
        "--skip-SNV-profiling": "",
        "--profile-SCVs": truw,
        "--description": "",
        "--skip-hierarchical-clustering": "",
        "--distance": "",
        "--linkage": "",
        "--min-contig-length": "",
        "--min-mean-coverage": "",
        "--min-coverage-for-variability": "",
        "--cluster-contigs": "",
        "--contigs-of-interest": "",
        "--queue-size": "",
        "--write-buffer-size": 10000,
        "--max-contig-length": "",
        "--max-coverage-depth": "",
        "--ignore-orphans": ""
    },
    "anvi_merge": {
        "--sample-name": "{group}",
        "--overwrite-output-destinations": true,
        "--description": "",
        "--skip-hierarchical-clustering": "",
        "--enforce-hierarchical-clustering": "",
        "--distance": "",
        "--linkage": "",
        "threads": ""
    },
    "import_percent_of_reads_mapped": {
        "run": true,
        "threads": ""
    },
    "krakenuniq": {
        "threads": 3,
        "--gzip-compressed": true,
        "additional_params": "",
        "run": "",
        "--db": "/scratch/genomics/scottjj/kraken_dbs/DB/"
    },
    "remove_short_reads_based_on_references": {
        "delimiter-for-iu-remove-ids-from-fastq": " ",
        "dont_remove_just_map": "",
        "references_for_removal_txt": "",
        "threads": ""
    },
    "anvi_cluster_contigs": {
        "--collection-name": "{driver}",
        "run": "",
        "--driver": "concoct",
        "--just-do-it": "",
        "--additional-params-concoct": "",
        "--additional-params-metabat2": "",
        "--additional-params-maxbin2": "",
        "--additional-params-dastool": "",
        "--additional-params-binsanity": "",
        "threads": 10
    },
    "gen_external_genome_file": {
        "threads": ""
    },
    "export_gene_calls_for_centrifuge": {
        "threads": ""
    },
    "anvi_import_taxonomy_for_genes": {
        "threads": ""
    },
    "annotate_contigs_database": {
        "threads": ""
    },
    "anvi_get_sequences_for_gene_calls": {
        "threads": ""
    },
    "gunzip_fasta": {
        "threads": ""
    },
    "reformat_external_gene_calls_table": {
        "threads": ""
    },
    "reformat_external_functions": {
        "threads": ""
    },
    "import_external_functions": {
        "threads": ""
    },
    "anvi_run_pfams": {
        "run": true,
        "--pfam-data-dir": "/pool/genomics/stri_istmobiome/dbs/pfam_db",
        "threads": 5
    },
    "iu_gen_configs": {
        "--r1-prefix": "",
        "--r2-prefix": "",
        "threads": ""
    },
    "gen_qc_report": {
        "threads": ""
    },
    "merge_fastqs_for_co_assembly": {
        "threads": ""
    },
    "merge_fastas_for_co_assembly": {
        "threads": ""
    },
    "bowtie_build": {
        "threads": ""
    },
    "anvi_init_bam": {
        "threads": ""
    },
    "krakenuniq_mpa_report": {
        "threads": ""
    },
    "import_krakenuniq_taxonomy": {
        "--min-abundance": "",
        "threads": ""
    },
    "anvi_summarize": {
        "additional_params": "",
        "run": "",
        "threads": ""
    },
    "anvi_split": {
        "additional_params": "",
        "run": "",
        "threads": ""
    },
    "references_mode": "",
    "all_against_all": "",
    "kraken_txt": "",
    "collections_txt": "",
    "output_dirs": {
        "FASTA_DIR": "02_FASTA",
        "CONTIGS_DIR": "03_CONTIGS",
        "QC_DIR": "01_QC",
        "MAPPING_DIR": "04_MAPPING",
        "PROFILE_DIR": "05_ANVIO_PROFILE",
        "MERGE_DIR": "06_MERGED",
        "TAXONOMY_DIR": "07_TAXONOMY",
        "SUMMARY_DIR": "08_SUMMARY",
        "SPLIT_PROFILES_DIR": "09_SPLIT_PROFILES",
        "LOGS_DIR": "00_LOGS"
    },
    "max_threads": "",
    "config_version": "1"
}