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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/phac-nml/viralassembly/master/nextflow_schema.json",
"title": "phac-nml/viralassembly pipeline parameters",
"description": "Assemble and QC viral reads",
"type": "object",
"definitions": {
"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 using either an input samplesheet or an input directory.",
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"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_pass": {
"type": "string",
"description": "Path to directory containing either barcoded fastq files or individually named fastq files",
"help_text": "Barcodes must be formatted as 'barcode##' to be found. Fastq files must end in '.fastq' or '.fastq.gz'",
"fa_icon": "fas fa-folder-open",
"format": "directory-path"
}
}
},
"important_input_values": {
"title": "Important input values",
"type": "object",
"fa_icon": "fas fa-sign-out-alt",
"description": "Important pipeline values for that are based on which variant caller is being used along with if any metadata is to be added",
"properties": {
"variant_caller": {
"type": "string",
"enum": [
"medaka",
"nanopolish",
"clair3"
],
"fa_icon": "fas fa-code",
"description": "Choose which variant caller to use. Options are 'medaka', 'clair3', and 'nanopolish'"
},
"metadata": {
"type": "string",
"fa_icon": "fas fa-file-csv",
"format": "file-path",
"mimetype": "text/plain",
"description": "Path to metadata TSV file containing at least columns 'sample' and 'barcode'"
},
"fast5_pass": {
"type": "string",
"format": "directory-path",
"fa_icon": "fas fa-folder",
"description": "Path to directory containing fast5 files for nanopolish",
"help_text": "Only for nanopolish"
},
"sequencing_summary": {
"type": "string",
"format": "file-path",
"fa_icon": "fas fa-file-alt",
"description": "Path to sequencing_summary file needed for nanopolish",
"help_text": "Only for nanopolish"
}
},
"required": [
"variant_caller"
]
},
"variant_model_settings": {
"title": "Variant model settings",
"type": "object",
"description": "Settings pertaining to the specific variant callers models. Be as accurate as possible for best results",
"default": "",
"fa_icon": "fas fa-tools",
"properties": {
"medaka_model": {
"type": "string",
"default": "r941_min_hac_g507",
"description": "Model to use in medaka. See medaka docs for more info"
},
"clair3_model": {
"type": "string",
"default": "r941_prom_sup_g5014",
"description": "Model to use in clair3. See clair3 docs for more info"
},
"clair3_user_variant_model": {
"type": "string",
"description": "Path to local clair3 model folder",
"format": "directory-path"
},
"clair3_no_pool_split": {
"type": "boolean",
"description": "Pass to not split amplicon pools when running clair3"
}
}
},
"read_filtering_options": {
"title": "Read filtering options",
"type": "object",
"description": "Options pertaining to how to filter reads",
"default": "",
"fa_icon": "fas fa-filter",
"properties": {
"min_reads": {
"type": "integer",
"default": 20,
"description": "Minimum reads required to run the sample after length filtering"
},
"min_length": {
"type": "integer",
"default": 200,
"description": "Minimum read length to keep"
},
"max_length": {
"type": "integer",
"default": 3000,
"description": "Maximum read length to keep"
}
}
},
"scheme_options": {
"title": "Scheme options",
"type": "object",
"description": "Options pertaining to the amplicon sequencing scheme. Scheme directories must include '*.scheme.bed' and '*.reference.fasta'",
"default": "",
"properties": {
"reference": {
"type": "string",
"description": "Path to local reference file to map to instead of using a primer scheme"
},
"scheme": {
"type": "string",
"default": "nCoV-2019",
"description": "Name of the pathogen to look for a scheme to use"
},
"scheme_version": {
"type": "string",
"default": "freed_nml_test_V2",
"description": "Name of the amplicon scheme"
},
"scheme_repo": {
"type": "string",
"default": "https://github.com/DarianHole/primer-schemes.git",
"description": "URL to the online scheme git repo to download"
},
"local_scheme": {
"type": "string",
"format": "directory-path",
"description": "Path to local scheme repo use instead of downloading"
}
}
},
"artic_minion_options": {
"title": "Artic minion options",
"type": "object",
"description": "Options pertaining to the steps in the artic minion pipeline",
"default": "",
"properties": {
"normalise": {
"type": "integer",
"default": 1000,
"description": "Normalize coverage",
"fa_icon": "fas fa-balance-scale"
},
"no_frameshift": {
"type": "boolean",
"description": "If passed, skip detected frameshift variants"
},
"use_bwa": {
"type": "boolean",
"description": "If passed, use BWA insead of minimap2 for read mapping"
},
"skip_longshot": {
"type": "boolean",
"description": "If passed, skip running longshot with medaka pipeline",
"fa_icon": "fas fa-forward"
},
"use_artic_tool": {
"type": "boolean",
"fa_icon": "fas fa-caret-right",
"description": "Pass to run tool artic pipeline instead of the nextflow adaptation this pipeline uses",
"help_text": "Clair3 always runs this"
}
}
},
"snpeff_options": {
"title": "SnpEff options",
"type": "object",
"description": "Options pertaining to running SnpEff for variant annotation",
"default": "",
"properties": {
"skip_snpeff": {
"type": "boolean",
"description": "If passed, skips running SnpEff",
"fa_icon": "fas fa-forward"
},
"gff": {
"type": "string",
"format": "file-path",
"description": "Path to gff3 formatted file to be used to build SnpEff database"
}
}
},
"qc_options": {
"title": "QC options",
"type": "object",
"description": "Options pertaining to QC outputs/stats",
"default": "",
"fa_icon": "fas fa-star",
"properties": {
"skip_qc": {
"type": "boolean",
"description": "If passed, skip running all QC and reporting steps",
"fa_icon": "fas fa-forward"
},
"pcr_primer_bed": {
"type": "string",
"format": "file-path",
"description": "Path to PCR Primer bed to check for any mutations occuring in defined regions"
},
"neg_control_threshold": {
"type": "number",
"default": 0.1,
"description": "Float threshold for a negative control sample to be considered contaminated"
},
"neg_ctrl_substrings": {
"type": "string",
"default": "neg,ntc,blank",
"description": "Control prefixes separated by a ',' to determine which samples are negative controls"
}
}
},
"report_generation_options": {
"title": "Report generation options",
"type": "object",
"description": "Options pertaining to final report generation",
"default": "",
"fa_icon": "fas fa-file-code",
"properties": {
"custom_report": {
"type": "boolean",
"description": "Create custom report instead of the MultiQC report (singularity not yet supported for custom reports)",
"fa_icon": "fas fa-file-signature"
},
"multiqc_config_overall": {
"type": "string",
"default": "$projectDir/assets/multiqc_config_overall.yaml",
"description": "MultiQC overall run config yaml file",
"format": "file-path"
},
"multiqc_config_sample": {
"type": "string",
"default": "$projectDir/assets/multiqc_config_sample.yaml",
"description": "MultiQC sample config yaml file",
"format": "file-path"
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are generic and don't quite all under any other categories",
"fa_icon": "fas fa-file-import",
"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"
},
"cache": {
"type": "string",
"help_text": "Path to directory to store or find environments/containers",
"fa_icon": "fas fa-folder",
"format": "directory-path",
"description": "Path to directory containing env/container shared store"
},
"help": {
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"show_hidden_params": {
"type": "boolean",
"hidden": true,
"fa_icon": "fas fa-minus-square"
}
},
"required": [
"outdir"
]
},
"resource_options": {
"title": "Resource options",
"type": "object",
"description": "Options pertaining to resource usage",
"default": "",
"fa_icon": "fas fa-cog",
"properties": {
"max_memory": {
"type": "string",
"default": "256.GB",
"description": "Maximum memory to use in pipeline for a single process. Given as a string with int.GB"
},
"max_cpus": {
"type": "integer",
"default": 16,
"description": "Maximum number of CPUs available to use for a single process"
},
"max_time": {
"type": "string",
"description": "Maximum time available for a single process to run with",
"default": "120.h"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_data_option_choose_1"
},
{
"$ref": "#/definitions/important_input_values"
},
{
"$ref": "#/definitions/variant_model_settings"
},
{
"$ref": "#/definitions/read_filtering_options"
},
{
"$ref": "#/definitions/scheme_options"
},
{
"$ref": "#/definitions/artic_minion_options"
},
{
"$ref": "#/definitions/snpeff_options"
},
{
"$ref": "#/definitions/qc_options"
},
{
"$ref": "#/definitions/report_generation_options"
},
{
"$ref": "#/definitions/generic_options"
},
{
"$ref": "#/definitions/resource_options"
}
]
}