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nextflow_schema.json
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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/main/nextflow_schema.json",
"title": "plant-food-research-open/assemblyqc pipeline parameters",
"description": "A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report.",
"type": "object",
"definitions": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"description": "",
"default": "",
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"description": "Input assembly sheet in CSV format",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open",
"default": "./results"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
}
},
"required": ["input", "outdir"]
},
"validation_options": {
"title": "Validation options",
"type": "object",
"description": "",
"default": "",
"properties": {
"check_sequence_duplicates": {
"type": "boolean",
"default": true,
"fa_icon": "fas fa-question-circle",
"description": "Check for duplicate sequences in fasta validation"
}
}
},
"general_stats_options": {
"title": "General stats options",
"type": "object",
"description": "",
"default": "",
"properties": {
"assemblathon_stats_n_limit": {
"type": "integer",
"default": 100,
"description": "The number of 'N's for the unknown gap size. NCBI recommendation is 100",
"fa_icon": "fas fa-ruler-horizontal"
}
}
},
"ncbi_fcs_options": {
"title": "NCBI FCS options",
"type": "object",
"description": "",
"default": "",
"properties": {
"ncbi_fcs_adaptor_skip": {
"type": "boolean",
"description": "Skip NCBI FCS Adaptor checking",
"default": true,
"fa_icon": "fas fa-forward"
},
"ncbi_fcs_adaptor_empire": {
"type": "string",
"enum": ["euk", "prok"],
"description": "Empire for NCBI FCS Adaptor checking: 'euk' for eukaryotes, or 'prok' for prokaryotes",
"fa_icon": "fas fa-project-diagram"
},
"ncbi_fcs_gx_skip": {
"type": "boolean",
"description": "Skip NCBI FCS external organism contamination checking",
"default": true,
"fa_icon": "fas fa-forward"
},
"ncbi_fcs_gx_tax_id": {
"type": "number",
"description": "Tax ID for NCBI FCS GX. See: https://www.ncbi.nlm.nih.gov/taxonomy",
"fa_icon": "fab fa-orcid"
},
"ncbi_fcs_gx_db_path": {
"type": "string",
"format": "directory-path",
"description": "Path to NCBI FCS GX database. See: https://github.com/ncbi/fcs/wiki/FCS-GX",
"fa_icon": "fas fa-folder-open"
},
"contamination_stops_pipeline": {
"type": "boolean",
"default": true,
"fa_icon": "fas fa-hand-paper",
"description": "Skip remaining QC steps for an assembly which has adaptor or GX contamination"
}
}
},
"busco_options": {
"title": "BUSCO options",
"type": "object",
"description": "",
"default": "",
"properties": {
"busco_skip": {
"type": "boolean",
"description": "Skip BUSCO",
"default": true,
"fa_icon": "fas fa-forward"
},
"busco_mode": {
"type": "string",
"enum": ["genome", "transcriptome", "proteins"],
"description": "BUSCO mode: 'genome', 'transcriptome', 'proteins'",
"fa_icon": "fas fa-cog"
},
"busco_lineage_datasets": {
"type": "string",
"pattern": "^(\\w+_odb10\\s)*\\w+_odb10$",
"description": "BUSCO lineages. It should be provided as a space-separated list of lineages: 'fungi_odb10 microsporidia_odb10'",
"fa_icon": "fas fa-clipboard-list"
},
"busco_download_path": {
"type": "string",
"description": "Download path for BUSCO",
"format": "directory-path",
"fa_icon": "fas fa-folder-open"
}
}
},
"tidk_options": {
"title": "TIDK options",
"type": "object",
"description": "",
"default": "",
"properties": {
"tidk_skip": {
"type": "boolean",
"description": "Skip telomere identification",
"default": true,
"fa_icon": "fas fa-forward"
},
"tidk_repeat_seq": {
"type": "string",
"description": "Telomere repeat sequence. Typical values for plant: TTTAGGG, fungus, vertebrates: TTAGGG and Insect: TTAGG",
"pattern": "^[ACGT]+$",
"fa_icon": "fas fa-dna"
},
"tidk_filter_by_size": {
"type": "boolean",
"description": "Filter assembly sequences smaller than the specified length",
"fa_icon": "fas fa-question-circle"
},
"tidk_filter_size_bp": {
"type": "integer",
"default": 1000000,
"description": "Filter size in base-pairs",
"fa_icon": "fas fa-ruler-horizontal"
}
}
},
"lai_options": {
"title": "LAI options",
"type": "object",
"description": "",
"default": "",
"properties": {
"lai_skip": {
"type": "boolean",
"default": true,
"description": "Skip LAI estimation",
"fa_icon": "fas fa-forward"
}
}
},
"kraken2_options": {
"title": "Kraken2 options",
"type": "object",
"description": "",
"default": "",
"properties": {
"kraken2_skip": {
"type": "boolean",
"default": true,
"description": "Skip Kraken2",
"fa_icon": "fas fa-forward"
},
"kraken2_db_path": {
"type": "string",
"description": "Kraken2 database path",
"format": "path",
"fa_icon": "fas fa-folder-open"
}
}
},
"hic_options": {
"title": "HiC options",
"type": "object",
"description": "",
"default": "",
"properties": {
"hic": {
"type": "string",
"description": "HiC reads path provided as a SRA ID or as paired reads such as 'hic_reads{1,2}.fastq.gz'",
"pattern": "^SR\\w+$|^\\S+\\{1,2\\}[\\w\\.]*\\.f(ast)?q\\.gz$"
},
"hic_skip_fastp": {
"type": "boolean",
"description": "Skip HiC read trimming",
"fa_icon": "fas fa-forward"
},
"hic_skip_fastqc": {
"type": "boolean",
"description": "Skip HiC read QC",
"fa_icon": "fas fa-forward"
},
"hic_fastp_ext_args": {
"type": "string",
"default": "--qualified_quality_phred 20 --length_required 50",
"description": "Additional parameters for fastp trimming",
"fa_icon": "fas fa-terminal"
}
}
},
"synteny_options": {
"title": "Synteny options",
"type": "object",
"description": "",
"default": "",
"properties": {
"synteny_skip": {
"type": "boolean",
"default": true,
"description": "Skip synteny analysis",
"fa_icon": "fas fa-forward"
},
"synteny_mummer_skip": {
"type": "boolean",
"default": true,
"description": "Skip Mummer-based synteny analysis",
"fa_icon": "fas fa-forward"
},
"synteny_plotsr_skip": {
"type": "boolean",
"default": true,
"description": "Skip plotsr-based synteny analysis",
"fa_icon": "fas fa-forward"
},
"synteny_xref_assemblies": {
"type": "string",
"description": "Reference assemblies for synteny analysis",
"format": "file-path",
"mimetype": "csv",
"schema": "assets/schema_xref_assemblies.json",
"fa_icon": "fas fa-file-csv"
},
"synteny_between_input_assemblies": {
"type": "boolean",
"description": "Create syntenic plots between each pair of input assemblies",
"default": true,
"fa_icon": "fas fa-question-circle"
},
"synteny_mummer_plot_type": {
"type": "string",
"default": "both",
"description": "Synteny plot type from Mummer alignments: 'dotplot', 'circos', or 'both'",
"enum": ["both", "dotplot", "circos"],
"fa_icon": "fas fa-chart-line"
},
"synteny_mummer_m2m_align": {
"type": "boolean",
"description": "Include Mummer alignment blocks with many-to-many mappings",
"fa_icon": "fas fa-question-circle"
},
"synteny_mummer_max_gap": {
"type": "integer",
"default": 1000000,
"description": "Mummer alignments within this distance are bundled together",
"fa_icon": "fas fa-ruler-horizontal"
},
"synteny_mummer_min_bundle_size": {
"type": "integer",
"default": 1000,
"description": "After bundling, any Mummer alignment bundle smaller than this size is filtered out",
"fa_icon": "fas fa-ruler-horizontal"
},
"synteny_plot_1_vs_all": {
"type": "boolean",
"description": "Create a separate synteny plot for each contig of the target assembly versus all contigs of the reference assembly. This only applies to Mummer plots",
"fa_icon": "fas fa-question-circle"
},
"synteny_color_by_contig": {
"type": "boolean",
"default": true,
"description": "Mummer synteny plots are colored by contig. Otherwise, they are colored by bundle size",
"fa_icon": "fas fa-question-circle"
},
"synteny_plotsr_seq_label": {
"type": "string",
"default": "Chr",
"description": "Sequence label prefix for plotsr synteny",
"fa_icon": "fas fa-tag"
},
"synteny_plotsr_assembly_order": {
"type": "string",
"fa_icon": "fas fa-sort-alpha-down",
"pattern": "^(\\w+\\s)*\\w+$",
"description": "The order in which the assemblies should be compared, provided as space separated string of assembly tags. If absent, assemblies are ordered by their tags alphabetically."
}
}
},
"merqury_options": {
"title": "Merqury options",
"type": "object",
"description": "",
"default": "",
"properties": {
"merqury_skip": {
"type": "boolean",
"default": true,
"description": "Skip merqury analysis",
"fa_icon": "fas fa-forward"
},
"merqury_kmer_length": {
"type": "integer",
"default": 21,
"description": "kmer length for merqury analysis",
"minimum": 3,
"fa_icon": "fas fa-ruler-horizontal"
}
}
},
"max_job_request_options": {
"title": "Max job request options",
"type": "object",
"fa_icon": "fab fa-acquisitions-incorporated",
"description": "Set the top limit for requested resources for any single job.",
"help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
"properties": {
"max_cpus": {
"type": "integer",
"description": "Maximum number of CPUs that can be requested for any single job.",
"default": 16,
"fa_icon": "fas fa-microchip",
"hidden": true
},
"max_memory": {
"type": "string",
"description": "Maximum amount of memory that can be requested for any single job. Example: '8.GB'",
"default": "512.GB",
"fa_icon": "fas fa-memory",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"hidden": true
},
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job. Example: '1.day'",
"default": "7.day",
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
"hidden": true
}
}
},
"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,
"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
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"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})$",
"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
},
"monochromeLogs": {
"type": "boolean",
"fa_icon": "fas fa-palette",
"description": "Do not use coloured log outputs.",
"hidden": true
},
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
"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
},
"validationFailUnrecognisedParams": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters fails when an unrecognised parameter is found.",
"hidden": true
},
"validationLenientMode": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters in lenient more.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/validation_options"
},
{
"$ref": "#/definitions/general_stats_options"
},
{
"$ref": "#/definitions/ncbi_fcs_options"
},
{
"$ref": "#/definitions/busco_options"
},
{
"$ref": "#/definitions/tidk_options"
},
{
"$ref": "#/definitions/lai_options"
},
{
"$ref": "#/definitions/kraken2_options"
},
{
"$ref": "#/definitions/hic_options"
},
{
"$ref": "#/definitions/synteny_options"
},
{
"$ref": "#/definitions/merqury_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/institutional_config_options"
},
{
"$ref": "#/definitions/generic_options"
}
]
}