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nextflow_schema.json
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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": "epi2me-labs/wf-artic",
"workflow_title": "Artic Network SARS-CoV-2 Analysis",
"description": "Run the ARTIC SARS-CoV-2 methodology on multiplexed MinION, GridION, and PromethION data.",
"demo_url": "https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-artic/wf-artic-demo.tar.gz",
"aws_demo_url": "https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-artic/wf-artic-demo/aws.nextflow.config",
"url": "https://github.com/epi2me-labs/wf-artic",
"type": "object",
"definitions": {
"input": {
"title": "Input Options",
"type": "object",
"fa_icon": "fas fa-arrow-right",
"description": "Parameters for finding and handling input data for analysis.",
"properties": {
"fastq": {
"type": "string",
"title": "FASTQ",
"format": "path",
"description": "FASTQ files to use in the analysis.",
"help_text": "This accepts one of three cases: (i) the path to a single FASTQ file; (ii) the path to a top-level directory containing FASTQ files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ files. In the first and second case, a sample name can be supplied with `--sample`. In the last case, the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`."
},
"analyse_unclassified": {
"type": "boolean",
"default": false,
"description": "Analyse unclassified reads from input directory. By default the workflow will not process reads in the unclassified directory.",
"help_text": "If selected and if the input is a multiplex directory the workflow will also process the unclassified directory."
},
"basecaller_cfg": {
"type": "string",
"title": "Basecaller configuration",
"description": "Name of the model that was used to basecall signal data, used to select an appropriate Medaka model.",
"help_text": "The basecaller configuration is used to automatically select the appropriate Medaka model. The automatic selection can be overridden with the 'medaka_variant_model' and 'medaka_consensus_model' parameters. The model list only shows models that are compatible with this workflow.",
"default": "dna_r9.4.1_450bps_hac",
"enum": [
"dna_r10.4.1_e8.2_400bps_hac@v3.5.2",
"dna_r10.4.1_e8.2_400bps_sup@v3.5.2",
"dna_r9.4.1_e8_fast@v3.4",
"dna_r9.4.1_e8_hac@v3.3",
"dna_r9.4.1_e8_sup@v3.3",
"dna_r10.4.1_e8.2_400bps_hac_prom",
"dna_r9.4.1_450bps_hac_prom",
"dna_r10.3_450bps_hac",
"dna_r10.3_450bps_hac_prom",
"dna_r10.4.1_e8.2_260bps_hac",
"dna_r10.4.1_e8.2_260bps_hac_prom",
"dna_r10.4.1_e8.2_400bps_hac",
"dna_r9.4.1_450bps_hac",
"dna_r9.4.1_e8.1_hac",
"dna_r9.4.1_e8.1_hac_prom"
]
}
},
"required": [
"fastq"
]
},
"primer_scheme_selection": {
"title": "Primer Scheme Selection",
"type": "object",
"fa_icon": "fas fa-code",
"description": "Reference genome related files and options required for the workflow.",
"properties": {
"scheme_name": {
"type": "string",
"default": "SARS-CoV-2",
"description": "Primer scheme name.",
"help_text": "This should be set to `SARS-CoV-2`, or `spike-seq` or your custom scheme name. This affects the choice of scheme versions you can use. The only scheme versions compatible with `spike-seq` are `ONT/V1` and `ONT/V4.1`"
},
"scheme_version": {
"type": "string",
"default": "ARTIC/V3",
"description": "Primer scheme version.",
"help_text": "This is the version of the primer scheme to use, more details about primer shemes can be found [here](https://labs.epi2me.io/ont-midnight-scheme-update/).",
"enum": [
"ARTIC/V1",
"ARTIC/V2",
"ARTIC/V3",
"ARTIC/V4",
"ARTIC/V4.1",
"ARTIC/V5.3.2",
"Midnight-ONT/V1",
"Midnight-ONT/V2",
"Midnight-ONT/V3",
"NEB-VarSkip/v2b",
"NEB-VarSkip/v1a-long",
"NEB-VarSkip/v2",
"NEB-VarSkip/v1a",
"Midnight-IDT/V1",
"Midnight-IDT/V2",
"ONT/V1",
"ONT/V4.1"
]
},
"custom_scheme": {
"type": "string",
"format": "path",
"description": "Path to a custom scheme.",
"help_text": "If you have a custom primer scheme you can enter the details here. This must be the full path to the directory containing your appropriately named scheme bed and fasta files; <SCHEME_NAME>.bed and <SCHEME_NAME>.fasta. More details [here](https://labs.epi2me.io/ont-midnight-scheme-update/)."
}
}
},
"samples": {
"title": "Sample Options",
"type": "object",
"fa_icon": "fas fa-vials",
"description": "Parameters that relate to samples such as sample sheets and sample names.",
"properties": {
"sample_sheet": {
"type": "string",
"format": "file-path",
"description": "A CSV file used to map barcodes to sample aliases. The sample sheet can be provided when the input data is a directory containing sub-directories with FASTQ files.",
"help_text": "The sample sheet is a CSV file with, minimally, columns named `barcode` and `alias`. Extra columns are allowed. A `type` column is required for certain workflows and should have the following values; `test_sample`, `positive_control`, `negative_control`, `no_template_control`."
},
"sample": {
"type": "string",
"description": "A single sample name for non-multiplexed data. Permissible if passing a single .fastq(.gz) file or directory of .fastq(.gz) files."
}
}
},
"output": {
"title": "Output Options",
"type": "object",
"fa_icon": "fas fa-arrow-left",
"description": "Parameters for saving and naming workflow outputs.",
"properties": {
"out_dir": {
"type": "string",
"default": "output",
"format": "directory-path",
"description": "Directory for output of all workflow results."
}
}
},
"reporting_options": {
"title": "Reporting Options",
"type": "object",
"description": "Options controlling report outputs",
"default": "",
"properties": {
"report_depth": {
"type": "integer",
"default": 100,
"description": "Min. depth for percentage coverage. (e.g. 89% genome covered at > `report_depth`)",
"minimum": 0,
"maximum": 100
},
"report_clade": {
"type": "boolean",
"default": true,
"description": "Show results of Nextclade analysis in report."
},
"report_coverage": {
"type": "boolean",
"default": true,
"description": "Show genome coverage traces in report."
},
"report_lineage": {
"type": "boolean",
"default": true,
"description": "Show results of Pangolin analysis in report."
},
"report_variant_summary": {
"type": "boolean",
"default": true,
"description": "Show variant information in report."
}
},
"fa_icon": "fas fa-address-card",
"help_text": ""
},
"advanced_options": {
"title": "Advanced Options",
"type": "object",
"fa_icon": "far fa-question-circle",
"description": "Advanced options for configuring processes inside the workflow.",
"help_text": "These advanced options do not need to be changed for typical use, but allow fine tuning of workflows for users who want more control over the workflow.",
"properties": {
"artic_threads": {
"type": "number",
"description": "Number of CPU threads to use per artic task.",
"help_text": "The total CPU resource used by the workflow is constrained by the executor configuration.",
"minimum": 1,
"default": 4
},
"pangolin_threads": {
"type": "number",
"description": "Number of CPU threads to use per pangolin task.",
"help_text": "The total CPU resource used by the workflow is constrained by the executor configuration.",
"minimum": 1,
"default": 4
},
"genotype_variants": {
"type": "string",
"description": "Report genotyping information for scheme's known variants of interest, optionally provide file path as argument."
},
"list_schemes": {
"type": "boolean",
"default": false,
"description": "List primer schemes and exit without running analysis."
},
"min_len": {
"type": "number",
"title": "Minimum read length",
"minimum": 50,
"maximum": 10000,
"description": "Minimum read length (default: set by scheme)."
},
"max_len": {
"type": "number",
"title": "Maximum read length",
"minimum": 50,
"maximum": 10000,
"description": "Maximum read length (default: set by scheme)."
},
"max_softclip_length": {
"type": "integer",
"title": "Maximum soft clip length",
"description": "Remove reads with alignments showing large soft clipping"
},
"update_data": {
"type": "boolean",
"default": true,
"description": "Update Pangolin and Nextclade data at runtime."
},
"pangolin_options": {
"type": "string",
"description": "Pass options to Pangolin, for example \"--analysis-mode fast --min-length 26000\"."
},
"nextclade_version": {
"type": "string",
"default": "2.14.0",
"description": "The version of nextclade",
"hidden": true
},
"nextclade_data_tag": {
"type": "string",
"description": "The tag of the nextclade data packet",
"hidden": false
},
"normalise": {
"type": "integer",
"default": 200,
"description": "Depth ceiling for depth of coverage normalisation"
},
"medaka_variant_model": {
"type": "string",
"description": "The name of a Medaka variant model to use. This name will override the model automatically chosen based on the provided basecaller configuration.",
"help_text": "The workflow will attempt to map the basecalling model used to a suitable Medaka variant model. You can override this by providing a model with this option instead."
}
}
},
"misc": {
"title": "Miscellaneous Options",
"type": "object",
"description": "Everything else.",
"default": "",
"properties": {
"lab_id": {
"type": "string",
"title": "Laboratory identifier",
"description": "Laboratory identifier, used in reporting."
},
"testkit": {
"type": "string",
"title": "Test kit identifier",
"description": "Test kit identifier, used in reporting."
},
"disable_ping": {
"type": "boolean",
"default": false,
"description": "Enable to prevent sending a workflow ping."
},
"help": {
"type": "boolean",
"default": false,
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"version": {
"type": "boolean",
"default": false,
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input"
},
{
"$ref": "#/definitions/primer_scheme_selection"
},
{
"$ref": "#/definitions/samples"
},
{
"$ref": "#/definitions/output"
},
{
"$ref": "#/definitions/reporting_options"
},
{
"$ref": "#/definitions/advanced_options"
},
{
"$ref": "#/definitions/misc"
}
],
"properties": {
"aws_image_prefix": {
"type": "string",
"hidden": true
},
"aws_queue": {
"type": "string",
"hidden": true
},
"_scheme_version": {
"type": "string",
"hidden": true
},
"_scheme_name": {
"type": "string",
"hidden": true
},
"_min_len": {
"type": "string",
"hidden": true
},
"_max_len": {
"type": "string",
"hidden": true
},
"_max_softclip_length": {
"type": "string",
"hidden": true
},
"_pangolin_options": {
"type": "string",
"hidden": true
},
"monochrome_logs": {
"type": "boolean"
},
"validate_params": {
"type": "boolean",
"default": true
},
"show_hidden_params": {
"type": "boolean"
}
},
"resources": {
"recommended": {
"cpus": 4,
"memory": "8GB"
},
"minimum": {
"cpus": 2,
"memory": "4GB"
},
"run_time": "5 minutes per sample",
"arm_support": false
},
"docs": {
"intro": "## Introduction\n\nThe wf-artic workflow implements a slightly modified ARTIC FieldBioinformatics\nworkflow for the purpose of preparing consensus sequences from SARS-CoV-2\ngenomes that have been DNA sequenced using a pooled tiling amplicon strategy.\n\nThe workflow consumes a folder containing demultiplexed sequence reads as\nprepared by either MinKNOW or Guppy. The workflow needs to know the primer\nscheme that has been used during genome amplification and library preparation\ne.g. ARTIC/V3 or ONT_Midnight/V1. Other parameters can be specified too e.g.\nassign sample names to the barcodes or to adjust the length distribution of\nacceptable amplicon sequences. The Medaka variant model is selected based on the\nprovided basecaller configuration (using the parameter `--basecaller_cfg`), or\nalternatively the Medaka model can be provided directly via the `--medaka_variant_model`\nparameter.\n\nDNA sequences in FASTQ format are aggregated, filtered for sequence length and\nquality characteristics and are mapped to the reference SARS-CoV-2 genome using\nminimap2. A primer-scheme specific bed file is used to identify the regions of\nthe mapped sequences that correspond to synthetic sequences (primers) - these\nregions are clipped to ensure that sequences are entirely of biological origin.\nThe retained sequences are used to prepare a consensus sequence that is then\npolished using Medaka and variant calling is performed to produce a VCF file of\ngenetic differences relative to the reference genome. The consensus sequence is\nannotated for virus clade information using NextClade and a strain assignment\nis performed using Pangolin.\n\nThe completed analysis is summarised in an HTML format report that summarises\nkey information that includes number of reads, depth of coverage information\nper amplicon and both the Nextclade and Pangolin information.\n\nMore information can be found in these two blog posts:\n* [SARS-CoV-2 Midnight Analysis](https://labs.epi2me.io/sarscov2-midnight-analysis/)\n* [Midnight Scheme Update](https://labs.epi2me.io/ont-midnight-scheme-update/)\n",
"links": "## Useful links\n\n* [Medaka](https://www.github.com/nanoporetech/medaka)\n* [Artic](https://github.com/artic-network/fieldbioinformatics)\n* [Nextflow](https://www.nextflow.io/)\n* [Docker](https://www.docker.com/products/docker-desktop)\n* [Singularity](https://docs.sylabs.io/guides/latest/user-guide/)\n"
}
}