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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/phac-nml/measeq/main/nextflow_schema.json",
"title": "phac-nml/measeq pipeline parameters",
"description": "Measles sequencing and analysis",
"type": "object",
"$defs": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"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"
},
"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"
}
}
},
"required_options": {
"title": "Required options",
"type": "object",
"description": "Options that are required to run the pipeline no matter what",
"default": "",
"properties": {
"platform": {
"type": "string",
"description": "Sequencing platform used. Options are: 'illumina' or 'nanopore'",
"enum": ["illumina", "nanopore"],
"fa_icon": "fas fa-vector-square"
}
},
"required": ["platform"],
"fa_icon": "fas fa-check"
},
"amplicon_options": {
"title": "Amplicon options",
"type": "object",
"description": "Options relating to running amplicon data",
"default": "",
"properties": {
"primer_bed": {
"type": "string",
"description": "Path to amplicon primer bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt"
},
"amplicon": {
"type": "boolean",
"description": "Run with amplicon data"
}
},
"fa_icon": "fas fa-vials"
},
"illumina_options": {
"title": "Illumina variant calling thresholds",
"type": "object",
"description": "Options specific to Illumina variant calling thresholds",
"default": "",
"properties": {
"remove_duplicates": {
"type": "boolean",
"description": "Mark and remove optical duplicates with picard markduplicates"
},
"ivar_trim_min_read_length": {
"type": "integer",
"description": "Minimum length of read to retain after trimming",
"default": 30,
"minimum": 0,
"fa_icon": "far fa-minus-square"
},
"ivar_primer_pairs": {
"type": "string",
"pattern": "^\\S+\\.tsv$",
"format": "file-path",
"description": "[Experimental] Path to iVar primer pair TSV information file containing left and right primer names for the same amplicon",
"fa_icon": "fas fa-file-csv",
"hidden": true
},
"ivar_offset": {
"type": "integer",
"description": "Reads that occur at the specified offset positions relative to primer positions will also be trimmed",
"default": 0,
"minimum": 0,
"fa_icon": "far fa-minus-square"
},
"min_ambiguity_threshold": {
"type": "number",
"description": "Minimum threshold to call a position as an IUPAC",
"default": 0.3,
"minimum": 0,
"maximum": 1,
"fa_icon": "far fa-minus-square"
},
"max_ambiguity_threshold": {
"type": "number",
"description": "Maximum threshold to call a position as an IUPAC",
"default": 0.75,
"minimum": 0,
"maximum": 1,
"fa_icon": "far fa-plus-square"
},
"min_indel_threshold": {
"type": "number",
"description": "Minimum thresholds to keep an indel",
"default": 0.6,
"minimum": 0,
"maximum": 1,
"fa_icon": "far fa-minus-square"
},
"min_alt_fraction_freebayes": {
"type": "number",
"description": "Require at least this fraction of observations supporting an alt allele to evaluate position",
"default": 0.05,
"minimum": 0,
"maximum": 1,
"fa_icon": "far fa-minus-square"
},
"min_variant_qual_freebayes": {
"type": "integer",
"description": "Minimum freebayes quality (probability) to filter variants",
"default": 20,
"minimum": 0,
"fa_icon": "far fa-minus-square"
},
"align_bowtie2": {
"type": "boolean",
"description": "Run illumina subworkflow with bowtie2 aligner instead of the default bwamem2 aligner",
"default": false
}
}
},
"nanopore_options": {
"title": "Nanopore options",
"type": "object",
"description": "Options specific to Nanopore data",
"default": "",
"properties": {
"model": {
"type": "string",
"description": "Clair3 model to use for variant calling. Will attempt to download the model",
"pattern": "^[A-Za-z0-9_\\-\\.]*$",
"fa_icon": "fab fa-modx"
},
"local_model": {
"type": "string",
"description": "Path to local clair3 model directory for variant calling",
"format": "directory-path",
"pattern": "^\\S+$",
"fa_icon": "fab fa-modx"
},
"ont_min_read_length": {
"type": "integer",
"default": 200,
"minimum": 0,
"description": "Minimum read length for input ONT reads"
},
"ont_min_base_qual": {
"type": "integer",
"default": 12,
"minimum": 0,
"description": "Minimum base quality of ONT reads to keep"
},
"normalise_ont": {
"type": "integer",
"default": 500,
"minimum": 0,
"description": "Normalise each amplicon barcode to set depth"
},
"ont_keep_incorrect_primers": {
"type": "boolean",
"default": false,
"description": "Keep reads with incorrect primer pairs"
},
"min_variant_qual_c3": {
"type": "integer",
"default": 7,
"minimum": 0,
"description": "Minimum variant quality to pass clair3 filters"
},
"min_frameshift_qual_c3": {
"type": "integer",
"default": 30,
"minimum": 0,
"description": "Minimum variant quality to pass clair3 filters"
},
"min_allele_freq_c3": {
"type": "number",
"default": 0.6,
"minimum": 0,
"maximum": 1,
"description": "Minimum alt allele frequency to pass a clair3 variant"
},
"min_mask_freq_c3": {
"type": "number",
"default": 0.3,
"minimum": 0,
"maximum": 1,
"description": "Minimum alt allele frequency to mask a variant as an N in the final consensus sequence"
},
"min_site_threshold_c3": {
"type": "number",
"default": 0.05,
"minimum": 0,
"maximum": 1,
"description": "Minimum overall site depth threshold for a variant to be included. So default 0.05 = a minimum of 5% of the positions depth for a variant to be included"
}
}
},
"analysis_options": {
"title": "Analysis options",
"type": "object",
"description": "Options related to the analysis of data or adding in data",
"default": "",
"properties": {
"reference": {
"type": "string",
"description": "Path to reference sequence to map measles fastqs to",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt"
},
"metadata": {
"type": "string",
"pattern": "^\\S+\\.tsv$",
"format": "file-path",
"description": "Path to metadata TSV file containing at minimum 'sample' column to add to final output",
"fa_icon": "fas fa-file-csv",
"hidden": true
},
"dsid_fasta": {
"type": "string",
"description": "Path to DSID multi-fasta to match output consensus data to",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt"
},
"min_depth": {
"type": "integer",
"default": 10,
"minimum": 0,
"description": "Minimum depth to call a base"
},
"no_frameshifts": {
"type": "boolean",
"description": "Fail all indel variants not divisible by 3"
},
"neg_control_pct_threshold": {
"type": "integer",
"default": 10,
"minimum": 0,
"maximum": 100,
"description": "Genome called threshold for negative control to be considered failed"
},
"neg_ctrl_substrings": {
"type": "string",
"pattern": "^[A-Za-z0-9_,\\-\\.]*$",
"default": "neg,ntc,blank,en",
"description": "Substrings to match to sample names to identify negative controls. Separated by a ,"
},
"skip_negative_grading": {
"type": "boolean",
"description": "Skip grading negative controls and give the run a PASS",
"fa_icon": "fas fa-forward"
}
}
},
"nextclade_options": {
"title": "Nextclade options",
"type": "object",
"description": "Options pertaining to nextclade datasets. These shouldn't be adjusted likely",
"default": "",
"properties": {
"nextclade_dataset_name": {
"type": "string",
"enum": ["nextstrain/measles/N450/WHO-2012"],
"default": "nextstrain/measles/N450/WHO-2012",
"description": "Name of the nextclade dataset to use. Shouldn't be changed unless needed"
},
"nextclade_dataset_tag": {
"type": "string",
"enum": ["2025-03-26--11-47-13Z"],
"default": "2025-03-26--11-47-13Z",
"description": "Tag for the nextclade dataset to use. Shouldn't be changed unless needed"
}
}
},
"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": {
"help": {
"type": "boolean",
"description": "Display help message and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"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
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
},
"trace_report_suffix": {
"type": "string",
"fa_icon": "far calendar",
"description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
"hidden": true
}
}
},
"contact_options": {
"title": "Contact information options",
"type": "object",
"description": "Options relating to contact information printing on final report",
"default": "",
"properties": {
"contact_name": {
"type": "string",
"description": "Name of the person or organization running the pipeline",
"fa_icon": "fas fa-vector-square",
"pattern": "^[A-Za-z0-9\\ _\\-\\.]*$"
},
"contact_website": {
"type": "string",
"description": "Website of the person or organization running the pipeline",
"fa_icon": "fas fa-vector-square",
"pattern": "^[A-Za-z0-9_\\-\\:\\/\\.\\%]*$"
},
"contact_phone": {
"type": "string",
"description": "Phone number of the person or organization running the pipeline",
"fa_icon": "fas fa-vector-square",
"pattern": "^[0-9+() _-]*$"
},
"contact_email": {
"type": "string",
"description": "Email of the person or organization running the pipeline",
"fa_icon": "fas fa-envelope",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
}
}
},
"reference_options": {
"title": "Reference options",
"type": "object",
"description": "Reference options when no specific reference is specified in the command",
"properties": {
"default_ref": {
"type": "string",
"description": "Path to D8 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"default_bed": {
"type": "string",
"description": "Path to D8 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"A_ref": {
"type": "string",
"description": "Path to A reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"A_bed": {
"type": "string",
"description": "Path to A primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"B1_ref": {
"type": "string",
"description": "Path to B1 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"B1_bed": {
"type": "string",
"description": "Path to B1 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"B2_ref": {
"type": "string",
"description": "Path to B2 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"B2_bed": {
"type": "string",
"description": "Path to B2 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"B3_ref": {
"type": "string",
"description": "Path to B3 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"B3_bed": {
"type": "string",
"description": "Path to B3 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"C1_ref": {
"type": "string",
"description": "Path to C1 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"C1_bed": {
"type": "string",
"description": "Path to C1 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"C2_ref": {
"type": "string",
"description": "Path to C2 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"C2_bed": {
"type": "string",
"description": "Path to C2 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D1_ref": {
"type": "string",
"description": "Path to D1 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D1_bed": {
"type": "string",
"description": "Path to D1 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D2_ref": {
"type": "string",
"description": "Path to D2 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D2_bed": {
"type": "string",
"description": "Path to D2 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D3_ref": {
"type": "string",
"description": "Path to D3 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D3_bed": {
"type": "string",
"description": "Path to D3 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D4_ref": {
"type": "string",
"description": "Path to D4 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D4_bed": {
"type": "string",
"description": "Path to D4 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D5_ref": {
"type": "string",
"description": "Path to D5 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D5_bed": {
"type": "string",
"description": "Path to D5 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D6_ref": {
"type": "string",
"description": "Path to D6 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D6_bed": {
"type": "string",
"description": "Path to D6 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D7_ref": {
"type": "string",
"description": "Path to D7 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D7_bed": {
"type": "string",
"description": "Path to D7 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D8_ref": {
"type": "string",
"description": "Path to D8 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D8_bed": {
"type": "string",
"description": "Path to D8 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D9_ref": {
"type": "string",
"description": "Path to D9 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D9_bed": {
"type": "string",
"description": "Path to D9 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D10_ref": {
"type": "string",
"description": "Path to D10 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D10_bed": {
"type": "string",
"description": "Path to D10 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D11_ref": {
"type": "string",
"description": "Path to D11 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"D11_bed": {
"type": "string",
"description": "Path to D11 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"E_ref": {
"type": "string",
"description": "Path to E reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"E_bed": {
"type": "string",
"description": "Path to E primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"F_ref": {
"type": "string",
"description": "Path to F reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"F_bed": {
"type": "string",
"description": "Path to F primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"G1_ref": {
"type": "string",
"description": "Path to G1 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"G1_bed": {
"type": "string",
"description": "Path to G1 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"G2_ref": {
"type": "string",
"description": "Path to G2 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"G2_bed": {
"type": "string",
"description": "Path to G2 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"G3_ref": {
"type": "string",
"description": "Path to G3 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"G3_bed": {
"type": "string",
"description": "Path to G3 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"H1_ref": {
"type": "string",
"description": "Path to H1 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"H1_bed": {
"type": "string",
"description": "Path to H1 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"H2_ref": {
"type": "string",
"description": "Path to H2 reference fasta",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-alt",
"hidden": true
},
"H2_bed": {
"type": "string",
"description": "Path to H2 primers bed file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/required_options"
},
{
"$ref": "#/$defs/amplicon_options"
},
{
"$ref": "#/$defs/illumina_options"
},
{
"$ref": "#/$defs/nanopore_options"
},
{
"$ref": "#/$defs/analysis_options"
},
{
"$ref": "#/$defs/nextclade_options"
},
{
"$ref": "#/$defs/generic_options"
},
{
"$ref": "#/$defs/contact_options"
},
{
"$ref": "#/$defs/reference_options"
}
]
}