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nextflow_schema.json
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nextflow_schema.json
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/UPHL-BioNGS/Cecret/master/nextflow_schema.json",
"title": "UPHL-BioNGS/Cecret pipeline parameters",
"description": "Reference-based consensus creation",
"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": ["outdir"],
"properties": {
"input": {
"type": "string",
"mimetype": "text/csv",
"description": "same as sample_sheet"
},
"sample_sheet": {
"type": "string",
"mimetype": "text/csv",
"description": "sample sheet with sample, fastq_1, and fastq_2 columns"
},
"reads": {
"type": "string",
"hidden": true,
"description": "Directory with paired-end fastq files"
},
"single_reads": {
"type": "string",
"hidden": true,
"description": "Directory with single-end illumina fastq files"
},
"nanopore": {
"type": "string",
"hidden": true,
"description": "Directory with nanopore fastq files"
},
"fastas": {
"type": "string",
"hidden": true,
"description": "input channel for fastas"
},
"multifastas": {
"type": "string",
"hidden": true,
"description": "input channel for multifasta files"
},
"sra_accessions": {
"type": "string",
"default": "[]",
"hidden": true,
"description": "list encased in [] brackets of fastq accessions to download from SRA/ENA (Illumina reads only)"
},
"genome_accessions": {
"type": "string",
"default": "[]",
"hidden": true,
"description": "list encased in [] brackets of genome accessions to download with datasets"
},
"species": {
"type": "string",
"default": "sarscov2",
"description": "specifies species-specific sub-workflows",
"enum": ["other", "mpx", "sarscov2"]
},
"vadr_reference": {
"type": "string",
"hidden": true,
"default": "sarscov2",
"description": "Specifies reference for vadr in container"
},
"nextclade_dataset": {
"type": "string",
"hidden": true,
"default": "sars-cov-2",
"description": "Specifies nextclade dataset"
},
"iqtree2_outgroup": {
"type": "string",
"hidden": true,
"default": "MN908947",
"description": "outgroup for multiple sequence alignment"
},
"minimum_depth": {
"type": "integer",
"default": 100,
"hidden": true,
"description": "minimum depth for calling a variant"
},
"mpileup_depth": {
"type": "integer",
"default": 8000,
"hidden": true,
"description": "number of reads put into memory by samtools/bcftools"
},
"kraken2_db": {
"type": "string",
"description": "directory to kraken2 database"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. Absolute paths are required on cloud infrastructure.",
"fa_icon": "fas fa-folder-open",
"default": "cecret"
}
}
},
"reference_files": {
"title": "Reference files",
"type": "object",
"description": "Files related to the reference genome",
"default": "",
"fa_icon": "fas fa-virus",
"properties": {
"reference_genome": {
"type": "string",
"description": "THE Reference genome"
},
"amplicon_bed": {
"type": "string",
"description": "Bedfile for amplicons"
},
"gff": {
"type": "string",
"description": "File used in ivar variants. Must correspond with reference genome."
},
"primer_bed": {
"type": "string",
"description": "File with bedfile of primers used in the analysis"
},
"primer_set": {
"type": "string",
"default": "ncov_V5.3.2",
"description": "Specifies a primer set included in repo",
"enum": [
"midnight_idt_V1",
"midnight_ont_V1",
"midnight_ont_V2",
"midnight_ont_V3",
"ncov_V3",
"ncov_V4",
"ncov_V4.1",
"ncov_V5.3.2",
"mpx_primalseq",
"mpx_idt"
]
}
}
},
"workflow_components": {
"title": "Workflow Components",
"type": "object",
"description": "The basic workflow components can be adjusted between some options",
"default": "",
"fa_icon": "fas fa-align-center",
"properties": {
"cleaner": {
"type": "string",
"default": "seqyclean",
"hidden": true,
"description": "Specifies what tool to use to remove low quality reads",
"enum": ["seqyclean", "fastp"]
},
"aligner": {
"type": "string",
"default": "bwa",
"hidden": true,
"description": "Specifies which aligner is going to be used.",
"enum": ["bwa", "minimap2"]
},
"trimmer": {
"type": "string",
"default": "ivar",
"hidden": true,
"description": "Specifies which tool to use to trim primers from primerbedfile",
"enum": ["samtools", "ivar", "none"]
},
"msa": {
"type": "string",
"default": "mafft",
"hidden": true,
"description": "Specifies what tool to use for multiple sequence alignment. Current options are only mafft."
},
"download_nextclade_dataset": {
"type": "boolean",
"default": true,
"description": "Uses included nextclade dataset for SARS-CoV-2 during runtime when false."
},
"filter": {
"type": "boolean",
"description": "Specifies if reference-mapped fastq files should be extracted"
},
"markdup": {
"type": "boolean",
"description": "Specifies if duplicate reads should be removed (not recommended for nanopore)"
},
"relatedness": {
"type": "boolean",
"description": "Turns on multiple sequence alignment subworkflow when true"
}
}
},
"toggles": {
"title": "Toggles",
"type": "object",
"description": "Toggles processes on (true)/off (false)",
"default": "",
"fa_icon": "fas fa-lock-open",
"properties": {
"aci": {
"type": "boolean",
"hidden": true,
"description": "Specifies if process should be used"
},
"artic": {
"type": "boolean",
"hidden": true,
"description": "Specifies if process should be used"
},
"artic_filter": {
"type": "boolean",
"hidden": true,
"description": "Specifies if process should be used"
},
"bbnorm": {
"type": "boolean",
"hidden": true,
"description": "Specifies if process should be used"
},
"bcftools_variants": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"fastqc": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"freyja": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"freyja_aggregate": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"heatcluster": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"igv_reports": {
"type": "boolean",
"hidden": true,
"description": "Specifies if process should be used"
},
"iqtree2": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"ivar_variants": {
"type": "boolean",
"hidden": false,
"description": "Specifies if process should be used"
},
"kraken2": {
"type": "boolean",
"hidden": true,
"description": "Specifies if process should be used"
},
"multiqc": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"nextclade": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"pango_aliasor": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"pangolin": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"phytreeviz": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"samtools_qc": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"samtools_ampliconstats": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"samtools_plot_ampliconstats": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"snpdists": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
},
"vadr": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Specifies if process should be used"
}
}
},
"process_adjustments": {
"title": "Process Adjustments",
"type": "object",
"description": "Adjusts how processes are run. These are similar to how task.ext values in modern nf-core workflows.",
"default": "",
"properties": {
"aci_options": {
"type": "string",
"default": "",
"hidden": true,
"description": "Options for process"
},
"artic_read_filtering_options": {
"type": "string",
"default": "--min-length 400 --max-length 700",
"hidden": true,
"description": "Options for process"
},
"artic_options": {
"type": "string",
"default": "--normalise 200 --skip-nanopolish --medaka --medaka-model r941_min_high_g360",
"hidden": true,
"description": "Options for process"
},
"bbnorm_options": {
"type": "string",
"default": "target=200 min=5",
"hidden": true,
"description": "Options for process"
},
"bcftools_variants_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"fastp_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"fastqc_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"filter_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"heatcluster_options": {
"type": "string",
"default": "-t png",
"hidden": true,
"description": "Options for process"
},
"igv_reports_options": {
"type": "string",
"default": "--flanking 1000",
"hidden": true,
"description": "Options for process"
},
"iqtree2_options": {
"type": "string",
"default": "-ninit 2 -n 2 -me 0.05 -m GTR",
"hidden": true,
"description": "Options for process"
},
"ivar_consensus_options": {
"type": "string",
"default": "-q 20 -t 0.6 -n N",
"hidden": true,
"description": "Options for process"
},
"ivar_trim_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"ivar_variants_options": {
"type": "string",
"default": "-q 20 -t 0.6",
"hidden": true,
"description": "Options for process"
},
"mafft_options": {
"type": "string",
"default": "--maxambiguous 0.5",
"hidden": true,
"description": "Options for process"
},
"minimap2_options": {
"type": "string",
"default": "-K 20M",
"hidden": true,
"description": "Options for process"
},
"multiqc_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"phytreeviz_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"pangolin_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"samtools_coverage_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"samtools_ampliconclip_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"samtools_flagstat_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"samtools_stats_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"samtools_ampliconstats_options": {
"type": "string",
"default": "--max-amplicon-length 3000 --max-amplicons 3000",
"hidden": true,
"description": "Options for process"
},
"samtools_plot_ampliconstats_options": {
"type": "string",
"default": "-size 1200,900 -size2 1200,900 -size3 1200,900",
"hidden": true,
"description": "Options for process"
},
"samtools_depth_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"samtools_markdup_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"samtools_fixmate_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"seqyclean_options": {
"type": "string",
"default": "-minlen 25 -qual",
"hidden": true,
"description": "Options for process"
},
"seqyclean_contaminant_file": {
"type": "string",
"default": "/Adapters_plus_PhiX_174.fasta",
"hidden": true,
"description": "Options for process"
},
"snpdists_options": {
"type": "string",
"default": "-c",
"hidden": true,
"description": "Options for process"
},
"nextclade_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"vadr_mdir": {
"type": "string",
"default": "/opt/vadr/vadr-models",
"hidden": true,
"description": "Options for process"
},
"freyja_demix_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"freyja_variants_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"pango_aliasor_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"freyja_aggregate_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"freyja_plot_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"freyja_plot_filetype": {
"type": "string",
"default": "png",
"hidden": true,
"description": "Options for process"
},
"kraken2_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"vadr_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
},
"vadr_trim_options": {
"type": "string",
"hidden": true,
"description": "Options for process"
}
}
},
"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"
}
}
},
"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
},
"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})$"
},
"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
},
"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
},
"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)."
},
"pipelines_testdata_base_path": {
"type": "string",
"fa_icon": "far fa-check-circle",
"description": "Base URL or local path to location of pipeline test dataset files",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/toggles"
},
{
"$ref": "#/$defs/process_adjustments"
},
{
"$ref": "#/$defs/workflow_components"
},
{
"$ref": "#/$defs/reference_files"
},
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/institutional_config_options"
},
{
"$ref": "#/$defs/generic_options"
},
{
"$ref": "#/$defs/generic_options"
}
]
}