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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/nf-core/pathogenseq/master/nextflow_schema.json",
"title": "nf-core/pathogenseq pipeline parameters",
"description": "pathogen sequence analysis",
"type": "object",
"definitions": {
"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",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"schema": "assets/schema_input.json",
"description": "Path to comma-separated samplesheet file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/pathogenseq/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"platform": {
"type": "string",
"fa_icon": "fas fa-hdd",
"default": "illumina",
"description": "Specifies the platform used to generate the sequences - available options are 'illumina|nanopore'.",
"enum": [
"illumina",
"nanopore"
]
},
"igenomes_ignore": {
"type": "boolean",
"fa_icon": "fas fa-hdd",
"description": "Whether ignore igenome configuration loading."
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"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"
}
}
},
"illumina_options": {
"title": "illumina_options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Illumina data analysis options",
"required": [
"illumina_reads_qc_tool",
"illumina_reads_assembler"
],
"properties": {
"illumina_reads_qc_tool": {
"type": "string",
"default": "fastp",
"description": "Specifies the reads triming and qc tool to use - available options are 'fastp|bbduk'.",
"fa_icon": "fas fa-cut",
"enum": [
"fastp",
"bbduk"
]
},
"illumina_reads_assembler": {
"type": "string",
"default": "unicycler",
"description": "Specifies the illumina reads assembly tool to use - available options are 'megahit|spades|skesa|unicycler|shovill'.",
"fa_icon": "fas fa-cut",
"enum": [
"megahit",
"spades",
"skesa",
"unicycler",
"shovill"
]
},
"min_tbp_for_assembly_illumina": {
"type": "integer",
"default": 1000000,
"description": "Required total basepairs of the reads to get into assembly stage.",
"fa_icon": "fas fa-cut"
},
"skip_illumina_reads_qc": {
"type": "boolean",
"default": false,
"description": "Skip illumina read quality control step.",
"fa_icon": "fas fa-cut"
},
"skip_illumina_dehost": {
"type": "boolean",
"default": false,
"description": "Skip illumina read quality control step.",
"fa_icon": "fas fa-cut"
},
"skip_illumina_reads_assembly": {
"type": "boolean",
"default": false,
"description": "Skip illumina read assembly step.",
"fa_icon": "fas fa-cut"
},
"hostile_human_ref_bowtie2": {
"type": "string",
"description": "hostile human genome index file",
"default": "/nfs/APL_Genomics/db/prod/hostile/bowtie2_indexes/human-t2t-hla-argos985"
}
}
},
"nanopore_options": {
"title": "nanopore_options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Nanopore reads data analysis options",
"properties": {
"hostile_human_ref_minimap2": {
"type": "string",
"description": "hostile human reference genome for minimap2",
"default": "/nfs/APL_Genomics/db/prod/hostile/minimap2_ref/human-t2t-hla-argos985.fa.gz"
},
"skip_nanopore_dehost": {
"type": "boolean",
"default": false,
"description": "Skip illumina read quality control step.",
"fa_icon": "fas fa-cut"
},
"nanopore_reads_assembler": {
"type": "string",
"default": "flye+medaka",
"description": "Specifies the nanopore reads assembly tool to use - available options are 'flye+medaka'.",
"fa_icon": "fas fa-cut"
},
"min_tbp_for_assembly_nanopore": {
"type": "integer",
"default": 1000000,
"description": "Required total basepairs of the reads to get into assembly stage.",
"fa_icon": "fas fa-cut"
},
"skip_polypolish": {
"type": "boolean",
"default": false,
"description": "Skip contig polish steps with illumina reads using polypolish tool.",
"fa_icon": "fas fa-cut"
},
"skip_polca": {
"type": "boolean",
"default": false,
"description": "Skip contig polish steps with illumina reads using polca tool.",
"fa_icon": "fas fa-cut"
},
"skip_nanopore_reads_qc": {
"type": "boolean",
"default": false,
"description": "Skip nanopore read quality control step.",
"fa_icon": "fas fa-cut"
},
"skip_nanopore_reads_assembly": {
"type": "boolean",
"default": false,
"description": "Skip nanopore read assembly step.",
"fa_icon": "fas fa-cut"
},
"skip_illumina_reads_polish": {
"type": "boolean",
"default": false,
"description": "Skip contig polishing steps with illumina reads.",
"fa_icon": "fas fa-cut"
}
}
},
"annotation_options": {
"title": "annotation_options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"properties": {
"bakta_db": {
"type": "string",
"default": "/nfs/APL_Genomics/db/prod/bakta/db",
"description": "Path to bakta database.",
"fa_icon": "fas fa-cut"
},
"checkm2_db": {
"type": "string",
"default": "/nfs/APL_Genomics/db/prod/CheckM2_database/uniref100.KO.1.dmnd",
"description": "Path to checkm2 database.",
"fa_icon": "fas fa-cut"
},
"amrfinderplus_db": {
"type": "string",
"default": "/nfs/APL_Genomics/db/prod/AMRFinderPlus/latest"
},
"skip_checkm2": {
"type": "boolean",
"default": false,
"description": "Skip checkm2 step.",
"fa_icon": "fas fa-cut"
},
"skip_bakta": {
"type": "boolean",
"default": false,
"description": "Skip bakta step.",
"fa_icon": "fas fa-cut"
},
"skip_mlst": {
"type": "boolean",
"default": false,
"description": "Skip mlst step.",
"fa_icon": "fas fa-cut"
},
"skip_mobsuite": {
"type": "boolean",
"default": false,
"description": "Skip skip_mobsuite step.",
"fa_icon": "fas fa-cut"
},
"skip_virulome": {
"type": "boolean",
"default": false,
"description": "Skip virulome step.",
"fa_icon": "fas fa-cut"
},
"skip_multiqc": {
"type": "boolean",
"default": false
},
"skip_amr": {
"type": "boolean",
"default": false,
"description": "Skip amr step.",
"fa_icon": "fas fa-cut"
},
"skip_depth_and_coverage_illumina": {
"type": "boolean",
"default": false,
"description": "Skip assembly depth calculation step with illumina reads.",
"fa_icon": "fas fa-cut"
},
"skip_depth_and_coverage_nanopore": {
"type": "boolean",
"default": false,
"description": "Skip assembly depth calculation step with nanopore reads.",
"fa_icon": "fas fa-cut"
}
}
},
"taxonomic_tool_options": {
"title": "taxonomic_tool_options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": [
"gambit_db",
"kraken2_db"
],
"properties": {
"kraken2_db": {
"type": "string",
"default": "/nfs/APL_Genomics/db/prod/kraken2/k2_standard_08gb_20220926",
"description": "Specify path to kraken2 database",
"fa_icon": "fas fa-cut"
},
"gambit_db": {
"type": "string",
"default": "/nfs/APL_Genomics/db/prod/gambit",
"description": "Path to gambit database.",
"fa_icon": "fas fa-cut"
},
"skip_illumina_kraken2": {
"type": "boolean",
"default": false,
"description": "Skip kraken2 with illumina reads step.",
"fa_icon": "fas fa-cut"
},
"skip_nanopore_kraken2": {
"type": "boolean",
"default": true,
"description": "Skip kraken2 with nanopore reads step.",
"fa_icon": "fas fa-cut"
},
"skip_gambit": {
"type": "boolean",
"default": false,
"description": "Skip gambit step.",
"fa_icon": "fas fa-cut"
}
}
},
"special_tool_options": {
"title": "special_tool_options",
"type": "object",
"fa_icon": "fas fa-terminal",
"help_text": "By default, those tools are all turned off.",
"description": "Define organism specific tools: Mycobacterium tuberculosis,Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus agalactiae gas.",
"properties": {
"gbssbg_db": {
"type": "string",
"default": "/nfs/APL_Genomics/db/prod/gbs-sbg/GBS-SBG.fasta",
"description": "Path to GBS-SBG database.",
"fa_icon": "fas fa-cut"
},
"skip_tbprofiler": {
"type": "boolean",
"default": true,
"description": "Skip Mycobacterium tuberculosis lineage and drug resistance analysis.",
"fa_icon": "fas fa-cut"
},
"skip_emmtyper": {
"type": "boolean",
"default": true,
"description": "Skip emm-typing of Streptococcus pyogenes.",
"fa_icon": "fas fa-cut"
},
"skip_pneumocat": {
"type": "boolean",
"default": true,
"description": "Skip capsular typing of Streptococcus pneumoniae using pneumocat.",
"fa_icon": "fas fa-cut"
},
"skip_gbssbg": {
"type": "boolean",
"default": true,
"description": "Skip serotyping of Streptococcus agalactiae using GBS-SBG.",
"fa_icon": "fas fa-cut"
}
}
},
"institutional_config_options": {
"title": "Institutional config options",
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
"help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_version": {
"type": "string",
"description": "Git commit id for Institutional configs.",
"default": "master",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"custom_config_base": {
"type": "string",
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
"help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"fa_icon": "fas fa-users-cog"
},
"config_profile_name": {
"type": "string",
"description": "Institutional config name.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_description": {
"type": "string",
"description": "Institutional config description.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_contact": {
"type": "string",
"description": "Institutional config contact information.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_url": {
"type": "string",
"description": "Institutional config URL link.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
}
}
},
"max_job_request_options": {
"title": "Max job request options",
"type": "object",
"fa_icon": "fab fa-acquisitions-incorporated",
"description": "Set the top limit for requested resources for any single job.",
"help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
"properties": {
"max_cpus": {
"type": "integer",
"description": "Maximum number of CPUs that can be requested for any single job.",
"default": 8,
"fa_icon": "fas fa-microchip",
"hidden": true,
"help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
},
"max_memory": {
"type": "string",
"description": "Maximum amount of memory that can be requested for any single job.",
"default": "64.GB",
"fa_icon": "fas fa-memory",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"hidden": true,
"help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
},
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job.",
"default": "240.h",
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
"hidden": true,
"help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
}
}
},
"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 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
},
"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
},
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"hidden": true
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true
},
"max_multiqc_email_size": {
"type": "string",
"description": "File size limit when attaching MultiQC reports to summary emails.",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"default": "25.MB",
"fa_icon": "fas fa-file-upload",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
"help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
},
"multiqc_config": {
"type": "string",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"multiqc_logo": {
"type": "string",
"description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
"fa_icon": "fas fa-image",
"hidden": true
},
"tracedir": {
"type": "string",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"default": "./results/pipeline_info",
"fa_icon": "fas fa-cogs",
"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
},
"validationShowHiddenParams": {
"type": "boolean",
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
},
"validationFailUnrecognisedParams": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters fails when an unrecognised parameter is found.",
"hidden": true,
"help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
},
"validationLenientMode": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters in lenient more.",
"hidden": true,
"help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
},
"show_hidden_params": {
"type": "boolean",
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/illumina_options"
},
{
"$ref": "#/definitions/nanopore_options"
},
{
"$ref": "#/definitions/annotation_options"
},
{
"$ref": "#/definitions/taxonomic_tool_options"
},
{
"$ref": "#/definitions/special_tool_options"
},
{
"$ref": "#/definitions/institutional_config_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/generic_options"
}
]
}