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tidying up
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@DOH-JDJ0303
DOH-JDJ0303 committed Feb 7, 2024
1 parent af09952 commit a32b84f
Showing 1 changed file with 89 additions and 70 deletions.
159 changes: 89 additions & 70 deletions nextflow_schema.json
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"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "refs", "outdir"],
"required": [
"input",
"refs",
"outdir"
],
"properties": {
"input": {
"type": "string",
Expand All @@ -34,65 +38,89 @@
"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"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"multiqc_title": {
"type": "string",
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature"
}
}
},
"assembly_options": {
"title": "Assembly options",
"classify_options": {
"title": "Classify options",
"type": "object",
"description": "",
"default": "",
"properties": {
"refs_meta": {
"mode": {
"type": "string",
"description": "Path to a .csv file containing taxonomic information about the provided references. This file is optional.",
"pattern": "^\\S+\\.csv$",
"format": "file-path"
"default": "accurate",
"description": "Reference selection mode ('fast' or 'accurate')",
"fa_icon": "fas fa-tachometer-alt"
},
"gen_frac": {
"type": "number",
"default": 0.75,
"description": "Minimum genome fraction for an assembly to be created"
}
}
},
"taxonomy_options": {
"title": "Taxonomy options",
"type": "object",
"description": "",
"default": "",
"properties": {
"assembler": {
"type": "string",
"default": "skesa",
"description": "Assembler to use for Shovill (skesa, spades, velvet, or megahit)"
"description": "Assembler to use for Shovill (skesa, spades, velvet, or megahit)",
"fa_icon": "fas fa-align-center"
},
"min_contig_cov": {
"type": "integer",
"default": 10,
"description": "Minimum contig coverage for Shovill"
"description": "Minimum contig coverage for Shovill",
"fa_icon": "fas fa-align-center"
},
"min_contig_len": {
"type": "integer",
"default": 300,
"description": "Minimum contig length for Shovill"
"description": "Minimum contig length for Shovill",
"fa_icon": "fas fa-align-center"
},
"gsize": {
"type": "string",
"default": "1.0M",
"description": "Approx. genome size for Shovill"
"description": "Approx. genome size for Shovill",
"fa_icon": "fas fa-align-center"
},
"avg_depth": {
"type": "integer",
"default": 100,
"fa_icon": "fas fa-align-center",
"description": "Minimum average depth of coverage for an assembly to be created. Only used in 'fast' mode."
},
"sm_db": {
"type": "string",
"default": "${baseDir}/assets/databases/genbank-2022.03-viral-k21.zip",
"fa_icon": "fas fa-bacteria",
"description": "Path to the Sourmash viral GenBank database."
}
}
},
"assembly_options": {
"title": "Assembly options",
"type": "object",
"description": "",
"default": "",
"properties": {
"gen_frac": {
"type": "number",
"default": 0.7,
"description": "Minimum genome fraction for an assembly to be created"
},
"ivar_t": {
"type": "number",
"default": 0.5,
"description": "Minimum depth to call consensus for ivar"
},
"ivar_q": {
"type": "integer",
"default": 20,
"description": "Minimum quality score threshold to count base for ivar"
},
"ivar_m": {
"type": "integer",
"default": 10,
"description": "Minimum frequency threshold(0 - 1) to call consensus for ivar"
},
"ivar_n": {
"type": "string",
"default": "N",
"description": "(N/-) Character to print in regions with less than minimum coverage for ivar"
}
}
},
Expand Down Expand Up @@ -204,7 +232,14 @@
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true
},
"email_on_fail": {
Expand Down Expand Up @@ -296,10 +331,10 @@
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/assembly_options"
"$ref": "#/definitions/classify_options"
},
{
"$ref": "#/definitions/taxonomy_options"
"$ref": "#/definitions/assembly_options"
},
{
"$ref": "#/definitions/institutional_config_options"
Expand All @@ -312,43 +347,27 @@
}
],
"properties": {
"mode": {
"multiqc_title": {
"type": "string",
"default": "accurate"
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature",
"hidden": true
},
"sm_db": {
"email": {
"type": "string",
"default": "/home/dev_env/vaper2/vaper/assets/databases/genbank-2022.03-viral-k21.zip"
},
"sm_taxa": {
"type": "string",
"default": "/home/dev_env/vaper2/vaper/assets/databases/genbank-2022.03-viral.lineages.csv.gz"
},
"ivar_q": {
"type": "integer",
"default": 20
},
"ivar_t": {
"type": "number",
"default": 0.5
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"hidden": true
},
"ivar_n": {
"igenomes_ignore": {
"type": "string",
"default": "N"
},
"ivar_m": {
"type": "integer",
"default": 10
"hidden": true
},
"genome": {
"type": "string"
},
"igenomes_ignore": {
"type": "string"
},
"avg_depth": {
"type": "integer",
"default": 100
"type": "string",
"hidden": true
}
}
}
}

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