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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/conf/schema/bactopia.json",
"title": "Bactopia pipeline parameters",
"description": "A flexible pipeline for complete analysis of bacterial genomes",
"type": "object",
"definitions": {
"input_parameters": {
"title": "Required Parameters",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"help_text": "",
"properties": {
"fastqs": {
"type": "string",
"format": "file-path",
"mimetype": "text/csv",
"description": "A FOFN with sample names and paths to FASTQ/FASTAs to process\n",
"help": "Created using `bactopia prepare`. Cannot be used with `--R1|--R2` or `--SE`",
"fa_icon": "fas fa-file-alt",
"header": "### For Procesessing Multiple Samples"
},
"R1": {
"type": "string",
"description": "First set of compressed (gzip) paired-end FASTQ reads (requires --R2 and --sample)",
"help": "Requires `--R2` and `--sample`. Cannot be used with `--fastqs` or `--SE` (unless `--hybrid` used).",
"fa_icon": "fas fa-file-archive",
"header": "### For Processing A Single Sample"
},
"R2": {
"type": "string",
"description": "Second set of compressed (gzip) paired-end FASTQ reads (requires --R1 and --sample)",
"help": "Requires `--R1` and `--sample`. Cannot be used with `--fastqs` or `--SE` (unless `--hybrid` used).",
"fa_icon": "fas fa-file-archive"
},
"SE": {
"type": "string",
"description": "Compressed (gzip) single-end FASTQ reads (requires --sample)",
"help": "Requires `--sample`. Cannot be used with `--fastqs` or `--R1|--R2` (unless `--hybrid` used).",
"fa_icon": "fas fa-file-archive"
},
"ont": {
"type": "boolean",
"description": "Treat `--SE` as long reads for analysis. (requires --sample)",
"fa_icon": "fas fa-level-up"
},
"hybrid": {
"type": "boolean",
"description": "Treat `--SE` as long reads for hybrid assembly. (requires --R1, --R2, --SE and --sample)",
"fa_icon": "fas fa-level-up"
},
"sample": {
"type": "string",
"description": "Sample name to use for the input sequences\n",
"help": "Required when using `--R1|--R2` or `--SE`",
"fa_icon": "fas fa-file"
},
"accessions": {
"type": "string",
"description": "A file containing ENA/SRA Experiment accessions or NCBI Assembly accessions to processed",
"fa_icon": "fas fa-file-alt",
"header": "### For Downloading from SRA/ENA or NCBI Assembly\n **Note: Downloaded assemblies will have error free Illumina reads simulated for processing.**"
},
"accession": {
"type": "string",
"description": "Sample name to use for the input sequences\n",
"help": "Required when using `--R1|--R2` or `--SE`",
"fa_icon": "fas fa-font"
},
"assembly": {
"type": "string",
"description": "A assembled genome in compressed FASTA format. (requires --sample)",
"help": "Error-free Illumina reads will be simulated for down stream processing",
"fa_icon": "fas fa-file-archive",
"header": "### For Processing an Assembly\n **Note: Assemblies will have error free Illumina reads simulated for processing.**"
}
}
},
"dataset_parameters": {
"title": "Dataset Parameters",
"type": "object",
"description": "",
"default": "",
"fa_icon": "fas fa-exclamation-circle",
"properties": {
"datasets": {
"type": "string",
"fa_icon": "fas fa-folder",
"description": "The path to datasets that have already been set up",
"help": "Bactopia Datasets are setup using `bactopia datasets`"
},
"species": {
"type": "string",
"description": "Name of species for species-specific dataset to use",
"help": "These datasets include MLST schemas, reference genomes, protein sets, etc...",
"fa_icon": "fas fa-bacterium"
},
"coverage": {
"type": "integer",
"default": 100,
"description": "Reduce samples to a given coverage",
"fa_icon": "fas fa-angle-double-down"
},
"genome_size": {
"type": "string",
"default": "0",
"description": "Expected genome size (bp) for all samples, a value of '0' will disable read error correction and read subsampling, otherwise estimate with Mash",
"help": "If `--species` is used, `min`, `median`, `mean`, or `max` can be used for `--genome_size`",
"fa_icon": "fas fa-arrows-alt-h"
},
"available_datasets": {
"type": "boolean",
"description": "Print a list of available datasets found based on location given by `--datasets`",
"fa_icon": "fas fa-print",
"hidden": true
}
}
},
"gather_samples_parameters": {
"title": "Gather Samples Parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"skip_fastq_check": {
"type": "boolean",
"description": "Skip minimum requirement checks for input FASTQs",
"help": "This parameter is useful if you are confident your sequences will pass the minimum requirements.",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"min_basepairs": {
"type": "integer",
"description": "The minimum amount of basepairs required to continue downstream analyses.",
"default": 2241820,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"min_reads": {
"type": "integer",
"description": "The minimum amount of reads required to continue downstream analyses.",
"default": 7472,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"min_coverage": {
"type": "integer",
"description": "The minimum amount of coverage required to continue downstream analyses.",
"default": 10,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"min_proportion": {
"type": "number",
"description": "The minimum proportion of basepairs for paired-end reads to continue downstream analyses.",
"help": "Example: If set to 0.75 the R1 and R2 must have > 75% proportion of reads (e.g. R1 100bp, R2 75bp, not R1 100bp, R2 50bp)",
"default": 0.5,
"fa_icon": "fas fa-balance-scale-left",
"hidden": true
},
"min_genome_size": {
"type": "integer",
"description": "The minimum estimated genome size allowed for the input sequence to continue downstream analyses.",
"default": 100000,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"max_genome_size": {
"type": "integer",
"description": "The maximum estimated genome size allowed for the input sequence to continue downstream analyses.",
"default": 18040666,
"fa_icon": "fas fa-angle-double-up",
"hidden": true
},
"attempts": {
"type": "integer",
"description": "Maximum times to attempt downloads",
"default": 3,
"fa_icon": "fas fa-redo",
"hidden": true
},
"use_ena": {
"type": "boolean",
"description": "Download FASTQs from ENA",
"fa_icon": "fas fa-globe-europe",
"hidden": true
},
"no_cache": {
"type": "boolean",
"description": "Skip caching the assembly summary file from ncbi-genome-download",
"fa_icon": "fas fa-save",
"hidden": true
}
}
},
"qc_reads_parameters": {
"title": "QC Reads Parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"skip_qc": {
"type": "boolean",
"description": "The QC step will be skipped and it will be assumed the inputs sequences have already been QCed.",
"help": "This is really only useful if you have already QC'd your reads, or have a specific need",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"skip_qc_plots": {
"type": "boolean",
"description": "QC Plot creation by FastQC or Nanoplot will be skipped",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"skip_error_correction": {
"type": "boolean",
"description": "FLASH error correction of reads will be skipped.",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"adapters": {
"type": "string",
"description": "A FASTA file containing adapters to remove",
"help": "By default, Bactopia will use the adapters provided by BBmap",
"fa_icon": "fas fa-file-alt",
"hidden": true
},
"adapter_k": {
"type": "integer",
"description": "Kmer length used for finding adapters.",
"help": "Adapters shorter than k will not be found",
"default": 23,
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"phix": {
"type": "string",
"description": "phiX174 reference genome to remove",
"help": "By default, use the phiX genome provided by BBmap",
"fa_icon": "fas fa-file-alt",
"hidden": true
},
"phix_k": {
"type": "integer",
"description": "Kmer length used for finding phiX174.",
"help": "Adapters shorter than k will not be found",
"default": 31,
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"ktrim": {
"type": "string",
"default": "r",
"description": "Trim reads to remove bases matching reference kmers",
"help": "Choices are: 'f' - do not trim, 'r' - trim ot the right, 'l' - trim to the left",
"fa_icon": "fas fa-boxes",
"hidden": true,
"enum": [
"f",
"r",
"l"
]
},
"mink": {
"type": "integer",
"description": "Look for shorter kmers at read tips down to this length, when k-trimming or masking.",
"help": "0 means disabled. Enabling this will disable maskmiddle",
"default": 11,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"hdist": {
"type": "integer",
"description": "Maximum Hamming distance for ref kmers (subs only)",
"help": "Memory use is proportional to (3*K)^hdist",
"default": 1,
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"tpe": {
"type": "string",
"default": "t",
"description": "When kmer right-trimming, trim both reads to the minimum length of either",
"help": "Choices are: 'f' - do not equally trim, 't' - equally trim ot the right",
"fa_icon": "fas fa-boxes",
"hidden": true,
"enum": [
"f",
"t"
]
},
"tbo": {
"type": "string",
"default": "t",
"description": "Trim adapters based on where paired reads overlap",
"help": "Choices are: 'f' - do not trim by overlap, 't' - trim by overlap",
"fa_icon": "fas fa-boxes",
"hidden": true,
"enum": [
"f",
"t"
]
},
"qtrim": {
"type": "string",
"default": "rl",
"description": "Trim read ends to remove bases with quality below trimq.",
"help": "Performed AFTER looking for kmers. Choices are: \n\n\t'rl' (trim both ends, Default)\n\t'f' (neither end)\n\t'r' (right end only)\n\t'l' (left end only)\n\t'w' (sliding window)",
"fa_icon": "fas fa-boxes",
"hidden": true,
"enum": [
"rl",
"f",
"r",
"l",
"w"
]
},
"trimq": {
"type": "integer",
"description": "Regions with average quality BELOW this will be trimmed if qtrim is set to something other than f",
"default": 6,
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"maq": {
"type": "integer",
"description": "Reads with average quality (after trimming) below this will be discarded",
"default": 10,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"minlength": {
"type": "integer",
"description": "Reads shorter than this after trimming will be discarded",
"help": "Pairs will be discarded if both are shorter",
"default": 35,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"ftm": {
"type": "integer",
"description": "If positive, right-trim length to be equal to zero, modulo this number",
"default": 5,
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"tossjunk": {
"type": "string",
"default": "t",
"description": "Discard reads with invalid characters as bases",
"help": "Choices are: 'f' - keep all reads, 't' - toss reads with ambiguous bases",
"fa_icon": "fas fa-boxes",
"hidden": true,
"enum": [
"f",
"t"
]
},
"qout": {
"type": "string",
"default": "33",
"description": "PHRED offset to use for output FASTQs",
"fa_icon": "fas fa-boxes",
"hidden": true,
"enum": [
"33",
"64"
]
},
"maxcor": {
"type": "integer",
"description": "Max number of corrections within a 20bp window",
"default": 1,
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"sampleseed": {
"type": "integer",
"description": "Set to a positive number to use as the random number generator seed for sampling",
"default": 42,
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"ont_minlength": {
"type": "integer",
"description": "ONT Reads shorter than this will be discarded",
"default": 1000,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"ont_minqual": {
"type": "integer",
"description": "Minimum average read quality filter of ONT reads",
"default": 0,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"porechop_opts": {
"type": "integer",
"description": "Extra Porechop options in quotes",
"help": "Example would be: '--adapter_threshold 50'",
"fa_icon": "fas fa-italic",
"hidden": true
},
"nanoplot_opts": {
"type": "integer",
"description": "Extra NanoPlot options in quotes",
"help": "Example would be: '--maxlength 10000'",
"fa_icon": "fas fa-italic",
"hidden": true
}
}
},
"assemble_genome_parameters": {
"title": "Assemble Genome Parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"shovill_assembler": {
"type": "string",
"default": "skesa",
"description": "Assembler to be used by Shovill",
"fa_icon": "fas fa-boxes",
"hidden": true,
"enum": [
"skesa",
"megahit",
"spades",
"velvet"
]
},
"dragonflye_assembler": {
"type": "string",
"default": "flye",
"description": "Assembler to be used by Dragonflye",
"fa_icon": "fas fa-boxes",
"hidden": true,
"enum": [
"flye",
"miniasm",
"raven"
]
},
"use_unicycler": {
"type": "boolean",
"description": "Use unicycler for paired end assembly",
"fa_icon": "fas fa-cut",
"hidden": true
},
"min_contig_len": {
"type": "integer",
"description": "Minimum contig length <0=AUTO>",
"default": 500,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"min_contig_cov": {
"type": "integer",
"description": "Minimum contig coverage <0=AUTO>",
"default": 2,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"contig_namefmt": {
"type": "string",
"description": "Format of contig FASTA IDs in 'printf' style",
"fa_icon": "fas fa-italic",
"hidden": true
},
"shovill_opts": {
"type": "string",
"description": "Extra assembler options in quotes",
"help": "Example for SPAdes would be: '--untrusted-contigs locus.fna'",
"fa_icon": "fas fa-italic",
"hidden": true
},
"shovill_kmers": {
"type": "string",
"description": "K-mers to use <blank=AUTO>",
"help": "This would allow you to specify the kmer lengths to be used",
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"trim": {
"type": "boolean",
"description": "Enable adaptor trimming",
"fa_icon": "fas fa-cut",
"hidden": true
},
"no_stitch": {
"type": "boolean",
"description": "Disable read stitching for paired-end reads",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"no_corr": {
"type": "boolean",
"description": "Disable post-assembly correction",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"unicycler_mode": {
"type": "string",
"default": "normal",
"description": "Bridging mode used by Unicycler",
"help": "Choices are:\n\n\tconservative = smaller contigs, lowest misassembly rate\n\tnormal = moderate contig size and misassembly rate (Default)\n\tbold = longest contigs, higher misassembly rate",
"fa_icon": "fas fa-boxes",
"hidden": true,
"enum": [
"conservative",
"normal",
"bold"
]
},
"min_polish_size": {
"type": "integer",
"description": "Contigs shorter than this value (bp) will not be polished using Pilon",
"default": 10000,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"min_component_size": {
"type": "integer",
"description": "Graph dead ends smaller than this size (bp) will be removed from the final graph",
"default": 1000,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"min_dead_end_size": {
"type": "integer",
"description": "Graph dead ends smaller than this size (bp) will be removed from the final graph",
"default": 1000,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"medaka_model": {
"type": "string",
"description": "The model to use for Medaka polishing",
"help": "This should be the same model used for base calling",
"fa_icon": "fas fa-font",
"hidden": true
},
"medaka_steps": {
"type": "integer",
"description": "The number of Medaka polishing steps to conduct",
"default": 0,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"racon_steps": {
"type": "integer",
"description": "The number of Racon polishing steps to conduct",
"default": 1,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"no_polish": {
"type": "boolean",
"description": "Skip the assembly polishing step",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"no_miniasm": {
"type": "boolean",
"description": "Skip miniasm+Racon bridging",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"no_rotate": {
"type": "boolean",
"description": "Do not rotate completed replicons to start at a standard gene",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"reassemble": {
"type": "boolean",
"hidden": true,
"description": "If reads were simulated, they will be used to create a new assembly.",
"fa_icon": "fas fa-redo"
}
}
},
"assembly_qc_parameters": {
"title": "Assembly QC Parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"run_checkm": {
"type": "boolean",
"description": "Run CheckM in the assembly QC step",
"fa_icon": "fas fa-play",
"hidden": true
},
"checkm_unique": {
"type": "integer",
"description": "Minimum number of unique phylogenetic markers required to use lineage-specific marker set.",
"default": 10,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"checkm_multi": {
"type": "integer",
"description": "Maximum number of multi-copy phylogenetic markers before defaulting to domain-level marker set.",
"default": 10,
"fa_icon": "fas fa-angle-double-up",
"hidden": true
},
"aai_strain": {
"type": "number",
"description": "AAI threshold used to identify strain heterogeneity",
"default": 0.9,
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"checkm_length": {
"type": "number",
"description": "Percent overlap between target and query",
"default": 0.7,
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"full_tree": {
"type": "boolean",
"description": "Use the full tree (requires ~40GB of memory) for determining lineage of each bin.",
"fa_icon": "fas fa-tree",
"hidden": true
},
"skip_pseudogene_correction": {
"type": "boolean",
"description": "Skip identification and filtering of pseudogene",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"ignore_thresholds": {
"type": "boolean",
"description": "Ignore model-specific score thresholds",
"fa_icon": "fas fa-eye-slash",
"hidden": true
},
"checkm_ali": {
"type": "boolean",
"description": "Generate HMMER alignment file for each bin",
"fa_icon": "fas fa-hard-hat",
"hidden": true
},
"checkm_nt": {
"type": "boolean",
"description": "Generate nucleotide gene sequences for each bin",
"fa_icon": "fas fa-hard-hat",
"hidden": true
},
"force_domain": {
"type": "boolean",
"description": "Use domain-level sets for all bins",
"fa_icon": "fas fa-hammer",
"hidden": true
},
"no_refinement": {
"type": "boolean",
"description": "Do not perform lineage-specific marker set refinement",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"individual_markers": {
"type": "boolean",
"description": "Treat marker as independent",
"fa_icon": "fas fa-check",
"hidden": true
},
"skip_adj_correction": {
"type": "boolean",
"description": "Do not exclude adjacent marker genes when estimating contamination",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"contig_thresholds": {
"type": "string",
"default": "0,1000,10000,100000,250000,1000000",
"description": "Comma-separated list of contig length thresholds",
"fa_icon": "fas fa-align-justify",
"hidden": true
},
"plots_format": {
"type": "string",
"default": "pdf",
"description": "Save plots in specified format",
"fa_icon": "fas fa-boxes",
"hidden": true,
"enum": [
"emf",
"eps",
"pdf",
"png",
"ps",
"raw",
"rgba",
"svg",
"svgz"
]
}
}
},
"annotate_genome_parameters": {
"title": "Annotate Genome Parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"compliant": {
"type": "boolean",
"description": "Force Genbank/ENA/DDJB compliance",
"fa_icon": "fas fa-check",
"hidden": true
},
"centre": {
"type": "string",
"default": "Bactopia",
"description": "Sequencing centre ID",
"fa_icon": "fas fa-school",
"hidden": true
},
"addmrna": {
"type": "boolean",
"description": "Add 'mRNA' features for each 'CDS' feature",
"fa_icon": "fas fa-check",
"hidden": true
},
"rawproduct": {
"type": "boolean",
"description": "Do not clean up /product annotation",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"cdsrnaolap": {
"type": "boolean",
"description": "Allow [tr]RNA to overlap CDS",
"fa_icon": "fas fa-check",
"hidden": true
},
"prokka_evalue": {
"type": "string",
"description": "Similarity e-value cut-off",
"default": "1e-09",
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"prokka_coverage": {
"type": "integer",
"description": "Minimum coverage on query protein",
"default": 80,
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"nogenes": {
"type": "boolean",
"description": "Do not add 'gene' features for each 'CDS' feature",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"norrna": {
"type": "boolean",
"description": "Don't run rRNA search",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"notrna": {
"type": "boolean",
"description": "Don't run tRNA search",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"rnammer": {
"type": "boolean",
"description": "Prefer RNAmmer over Barrnap for rRNA prediction",
"fa_icon": "fas fa-check",
"hidden": true
},
"rfam": {
"type": "boolean",
"description": "Enable searching for ncRNAs with Infernal+Rfam",
"fa_icon": "fas fa-check",
"hidden": true
},
"skip_prodigal_tf": {
"type": "boolean",
"description": "If a Prodigal training file was found, it will not be used",
"fa_icon": "fas fa-fast-forward",
"hidden": true
}
}
},
"call_variants_parameters": {
"title": "Call Variants Parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"mapqual": {
"type": "integer",
"description": "Minimum read mapping quality to consider",
"default": 60,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"basequal": {
"type": "integer",
"description": "Minimum base quality to consider",
"default": 13,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"mincov": {
"type": "integer",
"description": "Minimum site depth to for calling alleles",
"default": 10,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"minfrac": {
"type": "integer",
"description": "Minimum proportion for variant evidence (0=AUTO)",
"default": 0,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"minqual": {
"type": "integer",
"description": "Minimum QUALITY in VCF column 6",
"default": 100,
"fa_icon": "fas fa-angle-double-down",
"hidden": true
},
"maxsoft": {
"type": "integer",
"description": "Maximum soft clipping to allow",
"default": 10,
"fa_icon": "fas fa-angle-double-up",
"hidden": true
},
"bwaopt": {
"type": "string",
"description": "Extra BWA MEM options, eg. -x pacbio",
"fa_icon": "fas fa-italic",
"hidden": true
},
"fbopt": {
"type": "string",
"description": "Extra Freebayes options, eg. --theta 1E-6 --read-snp-limit 2",
"fa_icon": "fas fa-italic",
"hidden": true
},
"random_tie_break": {
"type": "boolean",
"description": "On references with matching distances, randomly select one.",
"fa_icon": "fas fa-check",
"hidden": true
},
"disable_auto_variants": {
"type": "boolean",
"description": "Disable automatic selection of reference genome based on Mash distances",
"fa_icon": "fas fa-fast-forward",
"hidden": true
}
}
},
"minmer_sketch_parameters": {
"title": "Minmer Sketch Parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"count_31mers": {
"type": "boolean",
"description": "Enable 31-mer counting with McCortex",
"fa_icon": "fas fa-check",
"hidden": true
},
"keep_singletons": {
"type": "boolean",
"description": "Keep all counted 31-mers",
"fa_icon": "fas fa-check",
"hidden": true
},
"mash_sketch": {
"type": "integer",
"description": "Sketch size. Each sketch will have at most this many non-redundant min-hashes.",
"default": 10000,
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"sourmash_scale": {
"type": "integer",
"description": "Choose number of hashes as 1 in FRACTION of input k-mers",
"default": 10000,
"fa_icon": "fas fa-hashtag",
"hidden": true
}
}
},
"minmer_query_parameters": {
"title": "Minmer Query Parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"no_winner_take_all": {
"type": "boolean",
"description": "Disable winner-takes-all strategy for identity estimates",
"help": "winner-take-all description: After counting hashes for each query, hashes that appear in multiple queries will be removed from all except the one with the best identity (ties broken by larger query), and other identities will be reduced. This removes output redundancy, providing a rough compositional outline.",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"screen_i": {
"type": "number",
"description": "Minimum identity to report.",
"help": "Inclusive unless set to zero, in which case only identities greater than zero (i.e. with at least one shared hash) will be reported. Set to -1 to output everything.",
"default": 0.8,
"fa_icon": "fas fa-hashtag",
"hidden": true
}
}
},
"mapping_query_parameters": {
"title": "Mapping Query Parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"keep_unmapped_reads": {
"type": "boolean",
"description": "Keep unmapped reads, this does not affect variant calling.",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"bwa_mem_opts": {
"type": "string",
"description": "Extra BWA MEM options",
"fa_icon": "fas fa-italic",
"hidden": true
},
"bwa_aln_opts": {
"type": "string",
"description": "Extra BWA ALN options",
"fa_icon": "fas fa-italic",
"hidden": true
},
"bwa_samse_opts": {
"type": "string",
"description": "Extra BWA SAMSE options",
"fa_icon": "fas fa-italic",
"hidden": true
},
"bwa_sampe_opts": {
"type": "string",
"description": "Extra BWA SAMPE options",
"fa_icon": "fas fa-italic",
"hidden": true
},
"bwa_n": {
"type": "integer",
"description": "Maximum number of alignments to output in the XA tag for reads paired properly.",
"help": "If a read has more than INT hits, the XA tag will not be written.",
"default": 9999,
"fa_icon": "fas fa-angle-double-up",
"hidden": true
}
}
},
"antimicrobial_resistance_parameters": {
"title": "Antimicrobial Resistance Parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"skip_amr": {
"type": "boolean",
"description": "Skip running AMRFinder+.",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"amr_plus": {
"type": "boolean",
"description": "Add the plus genes to the report",
"fa_icon": "fas fa-check",
"hidden": true
},
"amr_report_common": {
"type": "boolean",
"description": "Suppress proteins common to a taxonomy group",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"amr_organism": {
"type": "string",
"description": "Taxonomy group: Campylobacter, Escherichia, Klebsiella Salmonella, Staphylococcus, Vibrio",
"fa_icon": "fas fa-italic",