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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/Grandeur/master/nextflow_schema.json",
"title": "UPHL-BioNGS/Grandeur pipeline parameters",
"description": "Grandeur is short-read de novo assembly pipeline with serotyping.",
"type": "object",
"$defs": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": [
"outdir"
],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"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",
"hidden": true
},
"sample_sheet": {
"type": "string",
"description": "csv with sample,read1,read2"
},
"fastas": {
"type": "string",
"hidden": true,
"description": "directory with fasta files (not compatible with cloud resources)"
},
"fasta_list": {
"type": "string",
"description": "A sample sheet for fasta files"
},
"reads": {
"type": "string",
"hidden": true,
"description": "directory with paired-end illumina fastq files (not compatible with cloud resources)"
},
"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",
"default": "grandeur"
},
"sra_accessions": {
"type": "string",
"default": [],
"hidden": true,
"description": "list of accessions to download from the SRA"
},
"genome_accessions": {
"type": "string",
"default": [],
"hidden": true,
"description": "list of accessions to download from genomes"
},
"genome_sizes": {
"type": "string",
"default": null,
"hidden": true,
"description": "text of genome sizes"
}
}
},
"reference_files_paths": {
"title": "Reference files/paths",
"type": "object",
"description": "",
"default": "",
"properties": {
"kraken2_db": {
"type": "string",
"description": "directory of kraken2 database"
},
"blast_db": {
"type": "string",
"description": "directory of blast database. Compressed directories can be found at https://ftp.ncbi.nlm.nih.gov/blast/db/v5/."
},
"blast_db_type": {
"type": "string",
"description": "type of blast database (ex: 'nt', 'nt_prok', or 'ref_prok_rep_genomes')"
},
"mash_db": {
"type": "string",
"description": "prepared mash reference msh file"
},
"fastani_ref": {
"type": "string",
"description": "additional fasta files for fastani references"
},
"fastani_ref_list": {
"type": "string",
"description": "list of genomes (in fasta format) for fastani references"
}
}
},
"workflow_values": {
"title": "workflow values",
"type": "object",
"description": "",
"default": "",
"properties": {
"datasets_max_genomes": {
"type": "integer",
"default": 5,
"hidden": true,
"description": "the maxiumum number of genomes to download per organism"
},
"mash_max_hits": {
"type": "integer",
"default": 25,
"hidden": true,
"description": "the number of mash hits allowed in result file"
},
"min_core_genes": {
"type": "integer",
"default": 1500,
"description": "minimum number of genes in core genome alignment for iqtree2"
},
"iqtree2_outgroup": {
"type": "string",
"hidden": true,
"description": "to specify outgroup in iqtree2"
},
"minimum_reads": {
"type": "integer",
"default": 10000,
"hidden": true,
"description": "the minimum number of reads in a fastq file required to move to de novo alignment"
}
}
},
"subworkflow_toggles": {
"title": "Subworkflow toggles",
"type": "object",
"description": "",
"default": "",
"properties": {
"exclude_top_hit": {
"type": "boolean",
"hidden": true,
"description": "removes fastani top hit from msa"
},
"msa": {
"type": "boolean",
"description": "toggles whether or not phylogenetic analysis will be run on samples"
},
"aligner": {
"type": "string",
"default": "panaroo",
"hidden": true,
"description": "chooses core genome aligner (params.msa must be set to true)",
"enum": [
"roary",
"panaroo"
]
},
"annotator": {
"type": "string",
"default": "bakta",
"hidden": true,
"description": "chooses annotator (params.msa must be set to true)",
"enum": [
"bakta",
"prokka"
]
},
"skip_extras": {
"type": "boolean",
"hidden": true,
"description": "turns off blobtools, kraken2, fastani, mash, and report generation subworkflows"
},
"current_datasets": {
"type": "boolean",
"hidden": true,
"description": "toggles whether or not genomes are downloaded from NCBI"
}
}
},
"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": {
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"email_on_fail": {
"type": "string",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"plaintext_email": {
"type": "boolean",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"email": {
"type": "string",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"hook_url": {
"type": "string",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"pipelines_testdata_base_path": {
"type": "string",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"config_profile_description": {
"type": "string",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"config_profile_name": {
"type": "string",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"custom_config_version": {
"type": "string",
"default": "master",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"custom_config_base": {
"type": "string",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"config_profile_url": {
"type": "string",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"validationLenientMode": {
"type": "boolean",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"validationShowHiddenParams": {
"type": "boolean",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"validationFailUnrecognisedParams": {
"type": "boolean",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"config_profile_contact": {
"type": "string",
"description": "Stolen from example and might not do anything.",
"hidden": true
},
"validate_params": {
"type": "boolean",
"description": "Stolen from example and might not do anything.",
"fa_icon": "fas fa-check-square",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/reference_files_paths"
},
{
"$ref": "#/$defs/workflow_values"
},
{
"$ref": "#/$defs/subworkflow_toggles"
},
{
"$ref": "#/$defs/generic_options"
}
]
}