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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-mpx",
"workflow_title": "MPXV metagenomic assembly workflow",
"description": "Mpox metagenomics assembly from nanopore sequencing data.",
"demo_url": "https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-mpx/wf-mpx-demo.tar.gz",
"aws_demo_url": "https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-mpx/wf-mpx-demo/aws.nextflow.config",
"url": "https://github.com/epi2me-labs/wf-mpx",
"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": {
"bam": {
"type": "string",
"format": "file-path",
"title": "BAM",
"description": "BAM file to use in the analysis.",
"help_text": "Path to a single BAM file, or a single directory containing one or more BAM files. Multiple samples are not currently supported."
},
"fastq": {
"type": "string",
"format": "path",
"title": "FASTQ",
"description": "FASTQ file to use in the analysis.",
"help_text": "Path to a single FASTQ file, or a single directory containing one or more FASTQ files. Multiple samples or barcodes are not currently supported."
},
"reference": {
"type": "string",
"title": "Reference",
"description": "The reference genome to use for mapping.",
"help_text": "This is used if inputting a FASTQ file. We provide five MPXV reference sequences for alignment, representing clades I and II. More information can be found in our [blog post introducing this workflow](https://labs.epi2me.io/basic-mpox-workflow)",
"enum": [
"MN648051.1",
"MT903344.1",
"NC_003310.1",
"NC_063383.1",
"ON563414.1",
"ON568298.1"
],
"default": "NC_003310.1"
},
"reference_fasta": {
"type": "string",
"format": "path",
"title": "Reference",
"description": "A reference genome FASTA file to use for mapping.",
"help_text": "This is used if inputting a FASTQ file and when wanting to use a dfferent reference than the options provided with the workflow through the '--reference' parameter."
},
"reference_gb": {
"type": "string",
"format": "path",
"title": "Reference",
"description": "The reference genome genbank (.gb) file to use for mapping.",
"help_text": "This is used if inputting a FASTQ file and when wanting to use a dfferent reference than the options provided with the workflow through the '--reference' parameter."
}
},
"allOf": [
{
"oneOf": [
{
"required": ["fastq"]
},
{
"required": ["bam"]
}
]
},
{
"allOf": [
{
"if": {
"required": ["reference_fasta"]
},
"then": {
"required": ["reference_gb"]
}
},
{
"if": {
"required": ["reference_gb"]
},
"then": {
"required": ["reference_fasta"]
}
}
]
}
]
},
"samples": {
"title": "Sample Options",
"type": "object",
"fa_icon": "fas fa-vials",
"description": "Parameters that relate to samples.",
"properties": {
"sample": {
"type": "string",
"description": "A sample name for the outputs."
}
}
},
"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."
}
}
},
"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": {
"override_basecaller_cfg": {
"type": "string",
"title": "Override basecaller configuration",
"description": "Override auto-detected basecaller model that processed the signal data; used to select an appropriate Medaka model.",
"help_text": "Per default, the workflow tries to determine the basecall model from the input data. This parameter can be used to override the detected value (or to provide a model name if none was found in the inputs). However, users should only do this if they know for certain which model was used as selecting the wrong option might give sub-optimal results. A list of recent models can be found here: https://github.com/nanoporetech/dorado#DNA-models.",
"enum": [
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0",
"dna_r10.4.1_e8.2_400bps_sup@v4.3.0",
"dna_r10.4.1_e8.2_400bps_hac@v4.3.0",
"dna_r10.4.1_e8.2_400bps_sup@v4.2.0",
"dna_r10.4.1_e8.2_400bps_hac@v4.2.0",
"dna_r10.4.1_e8.2_260bps_hac@v4.1.0",
"dna_r10.4.1_e8.2_260bps_sup@v4.1.0",
"dna_r10.4.1_e8.2_400bps_hac@v4.1.0",
"dna_r10.4.1_e8.2_400bps_sup@v4.1.0",
"dna_r10.4.1_e8.2_260bps_hac@v4.0.0",
"dna_r10.4.1_e8.2_260bps_sup@v4.0.0",
"dna_r10.4.1_e8.2_400bps_hac@v4.0.0",
"dna_r10.4.1_e8.2_400bps_sup@v4.0.0",
"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"
]
},
"assembly": {
"type": "boolean",
"description": "Perform assembly with flye.",
"help_text": "Take the reads mapped to the mpx reference and perform a de novo assembly using Flye. This might be useful to uncover any structural variation not present in your chosen reference genome. Turning off will reduce run times and computational intensity at the expense of not being able to identify structural variants.",
"default": true
},
"min_coverage": {
"type": "number",
"title": "Minimum coverage",
"description": "Coverage threshold for masking in the consensus step.",
"help_text": "Regions with less than the coverage entered here are masked (nucleotide sequences will be replaced with N) when generating the consensus. It might be useful to decrease this value if you have very low coverage, but this will affect the quality of your consensus sequence.",
"minimum": 1,
"default": 20
}
}
},
"misc": {
"title": "Miscellaneous Options",
"type": "object",
"description": "Everything else.",
"default": "",
"properties": {
"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
},
"store_dir": {
"type": "string",
"description": "Unused.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input"
},
{
"$ref": "#/definitions/samples"
},
{
"$ref": "#/definitions/output"
},
{
"$ref": "#/definitions/advanced_options"
},
{
"$ref": "#/definitions/misc"
}
],
"properties": {
"aws_image_prefix": {
"type": "string",
"hidden": true
},
"aws_queue": {
"type": "string",
"hidden": true
},
"_reference": {
"type": "string",
"hidden": true
},
"_genbank": {
"type": "string",
"hidden": true
},
"monochrome_logs": {
"type": "boolean"
},
"validate_params": {
"type": "boolean",
"default": true
},
"show_hidden_params": {
"type": "boolean"
}
},
"resources": {
"recommended": {
"cpus": 4,
"memory": "32GB"
},
"minimum": {
"cpus": 4,
"memory": "32GB"
},
"run_time": "45 minutes",
"arm_support": false
}
}