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nextflow_schema.json
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/phac-nml/legiovue/main/nextflow_schema.json",
"title": "phac-nml/LegioVue pipeline parameters",
"description": "Legionella pneumophila WGS analysis",
"type": "object",
"$defs": {
"input_data_option_choose_1": {
"title": "Input data option (choose 1)",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data",
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",
"fa_icon": "fas fa-file-csv"
},
"fastq_dir": {
"type": "string",
"fa_icon": "fas fa-folder-open",
"description": "Path to directory containing paired (_R1/_R2) gzipped fastq files",
"format": "directory-path",
"hidden": true
}
}
},
"filtering_options": {
"title": "Filtering options",
"type": "object",
"description": "Options on minimum values for filtering out input data",
"default": "",
"properties": {
"kraken2_db": {
"type": "string",
"exists": true,
"format": "directory-path",
"fa_icon": "fas fa-server",
"description": "Path to kraken2 database to use for abundance checks"
},
"min_abundance_percent": {
"type": "number",
"default": 10,
"description": "Minimum L.pn abundance to keep sample in pipeline",
"fa_icon": "fas fa-percentage",
"minimum": 0,
"maximum": 100
},
"min_reads": {
"type": "integer",
"default": 60000,
"description": "Minimum number of paired reads to keep sample in pipeline",
"minimum": 0
}
},
"required": ["kraken2_db"],
"fa_icon": "fas fa-filter"
},
"skipping_options": {
"title": "Step skipping options",
"type": "object",
"description": "Processes that can be skipped through specifying the following parameters",
"default": "",
"properties": {
"skip_el_gato": {
"type": "boolean",
"description": "Skip running all el_gato sequence typing aspects",
"fa_icon": "fas fa-forward"
},
"skip_plotting": {
"type": "boolean",
"description": "Skip plotting el_gato allele profiles",
"fa_icon": "fas fa-forward"
}
},
"fa_icon": "fas fa-forward"
},
"quast_and_quality_options": {
"title": "QUAST and Quality options",
"type": "object",
"description": "Options for adjusting running QUAST",
"default": "",
"properties": {
"quast_ref": {
"type": "string",
"default": "data/C9_S.reference.fna",
"format": "file-path",
"fa_icon": "fas fa-file-alt",
"description": "Path to reference fasta file to base QUAST alignment metrics off of",
"hidden": true
},
"max_contigs": {
"type": "integer",
"default": 100,
"description": "Threshold for the number of contigs > 500bp assembled by SPAdes to get scoring points",
"minimum": 0
},
"min_align_percent": {
"type": "number",
"default": 75,
"description": "Thresold for minimum QUAST genome fraction percentage to get scoring points",
"fa_icon": "fas fa-percentage",
"minimum": 0,
"maximum": 100
},
"min_reads_warn": {
"type": "integer",
"default": 150000,
"description": "Threshold for minimum number of reads that will be given a QC warning",
"minimum": 0
},
"min_n50_score": {
"type": "integer",
"default": 80000,
"description": "Thresold for minimum QUAST N50 value to obtain scoring points",
"minimum": 0
},
"max_n50_score": {
"type": "integer",
"default": 220000,
"description": "Thresold for maximum QUAST N50 score to get max scoring points",
"minimum": 0
}
}
},
"chewbbaca_options": {
"title": "ChewBBACA options",
"type": "object",
"description": "Specifies the input for the chewBBACA schema to utilize for cgMLST",
"default": "",
"properties": {
"schema_targets": {
"type": "string",
"description": "ChewBBACA schema targets directory",
"format": "directory-path",
"hidden": true
},
"prepped_schema": {
"type": "string",
"default": "data/SeqSphere_1521_schema",
"description": "ChewBBACA prepped schema directory",
"format": "directory-path",
"hidden": true
}
},
"fa_icon": "fab fa-cc-diners-club"
},
"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": {
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open",
"default": "results"
},
"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
},
"max_memory": {
"type": "string",
"default": "128.GB",
"fa_icon": "fas fa-database",
"description": "Maximum memory to allow for a process to assign",
"hidden": true
},
"max_cpus": {
"type": "integer",
"default": 16,
"fa_icon": "fas fa-microchip",
"description": "Maximum CPUs to allow for a process to assign",
"hidden": true
},
"max_time": {
"type": "string",
"default": "240.h",
"fa_icon": "fas fa-clock",
"description": "Maximum time to allow for a process to assign",
"hidden": true
},
"help": {
"type": "boolean",
"description": "Display help info and exit",
"fa_icon": "far fa-question-circle",
"hidden": true
},
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
}
},
"required": ["outdir"]
}
},
"allOf": [
{
"$ref": "#/$defs/input_data_option_choose_1"
},
{
"$ref": "#/$defs/filtering_options"
},
{
"$ref": "#/$defs/skipping_options"
},
{
"$ref": "#/$defs/quast_and_quality_options"
},
{
"$ref": "#/$defs/chewbbaca_options"
},
{
"$ref": "#/$defs/generic_options"
}
]
}