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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
"title": ". pipeline parameters",
"description": "",
"type": "object",
"definitions": {
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/generic_options"
}
],
"properties": {
"samplesheet": {
"type": "string",
"description": "samplesheet",
"default": "''"
},
"enable_conda": {
"type": "boolean",
"description": "use conda (not supported)"
},
"collect": {
"type": "boolean",
"description": "combine reads from multiple fastq files into one?"
},
"skip_flye": {
"type": "boolean",
"description": "skip flye assembly"
},
"skip_alignments": {
"type": "boolean",
"description": "skip alignment to initial assembly and reference"
},
"flye_mode": {
"type": "string",
"default": "'--nano-hq'",
"description": "flye mode to use"
},
"flye_args": {
"type": "string",
"default": "''",
"description": "extra args for flye"
},
"polish_pilon": {
"type": "boolean",
"description": "use pilon to polish with short reads"
},
"medaka_model": {
"type": "string",
"default": "'[email protected]:consesus'",
"description": "medaka model to use"
},
"lift_annotations": {
"type": "boolean",
"description": "run liftoff to lift over annotations"
},
"out": {
"type": "string",
"default": "'./out'",
"description": "results directory"
},
"scaffold_ragtag": {
"type": "boolean",
"description": "Scaffold with ragtag"
},
"scaffold_links": {
"type": "boolean",
"description": "Scaffold with links"
},
"scaffold_longstitch": {
"type": "boolean",
"description": "Scaffold with longstitch"
},
"busoc_db": {
"type": "string",
"default": "/dss/dsslegfs01/pn73so/pn73so-dss-0000/becker_common/software/busco_db",
"description": "path to busco db"
},
"porechop": {
"type": "boolean",
"description": "run porechop"
},
"use_ref": {
"type": "boolean",
"description": "Use a reference genome",
"default": true
},
"busco_lineage": {
"type": "string",
"description": "busco lineage to use",
"default": "\"brassicales_odb10\""
},
"jelly_is_reads": {
"type": "string",
"description": "not used",
"hidden": true
},
"kmer_length": {
"type": "integer",
"description": "k-mer length",
"default": 21
},
"read_length": {
"type": "integer",
"description": "read length (if null, estimate)"
},
"dump": {
"type": "boolean",
"description": "Dump kmers from jellyfish"
},
"genome_size": {
"type": "integer",
"description": "Expected genome size, if null estimate from kmers"
},
"hifi": {
"type": "boolean",
"description": "HiFi reads available?"
},
"lima": {
"type": "boolean",
"description": "Use lima on hifi reads"
},
"pacbio_primers": {
"type": "string",
"description": "File containing pacbio primers"
},
"hifi_ont": {
"type": "boolean",
"description": "Merge hifi and ont reads"
},
"hifi_only": {
"type": "boolean",
"description": "Only hifi reads"
},
"hifi_args": {
"type": "string",
"description": "Extra arguments for hifiasm"
},
"polish_medaka": {
"type": "string",
"description": "polish with medaka"
}
},
"required": [
"samplesheet"
]
}