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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/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",
"$defs": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"description": "",
"default": "",
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"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"
},
"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"
},
"gfastats_skip": {
"type": "boolean",
"description": "Skip Gfastats",
"default": true,
"fa_icon": "fas fa-forward"
}
}
},
"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"
}
}
},
"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"
}
}
},
"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$",
"description": "BUSCO lineages. It should be provided as a space-separated list of lineages: 'fungi_odb10 microsporidia_odb10'",
"fa_icon": "fas fa-clipboard-list"
},
"busco_download_path": {
"type": "string",
"description": "Download path for BUSCO",
"format": "directory-path",
"fa_icon": "fas fa-folder-open"
}
}
},
"lai_options": {
"title": "LAI options",
"type": "object",
"description": "",
"default": "",
"properties": {
"lai_skip": {
"type": "boolean",
"default": true,
"description": "Skip LAI estimation",
"fa_icon": "fas fa-forward"
}
}
},
"kraken2_options": {
"title": "Kraken 2 options",
"type": "object",
"description": "",
"default": "",
"properties": {
"kraken2_skip": {
"type": "boolean",
"default": true,
"description": "Skip Kraken2",
"fa_icon": "fas fa-forward"
},
"kraken2_db_path": {
"type": "string",
"description": "Kraken2 database path",
"format": "path",
"fa_icon": "fas fa-folder-open"
}
}
},
"hic_options": {
"title": "HiC options",
"type": "object",
"description": "",
"default": "",
"properties": {
"hic": {
"type": "string",
"description": "HiC reads path provided as a SRA ID or as paired reads such as 'hic_reads{1,2}.fastq.gz'",
"pattern": "^SR\\w+$|^\\S+\\{1,2\\}[\\w\\.]*\\.f(ast)?q\\.gz$",
"fa_icon": "fas fa-copy"
},
"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"
},
"hic_samtools_ext_args": {
"type": "string",
"default": "-F 3852",
"fa_icon": "fas fa-terminal",
"description": "Additional parameters for samtools view command run after samblaster"
}
}
},
"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"
}
}
},
"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": 1000000,
"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."
}
}
},
"orthofinder_options": {
"title": "OrthoFinder options",
"type": "object",
"description": "",
"default": "",
"properties": {
"orthofinder_skip": {
"type": "boolean",
"default": true,
"fa_icon": "fas fa-forward",
"description": "Skip orthofinder"
}
}
},
"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"
}
}
},
"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": "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})$",
"hidden": true
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/validation_options"
},
{
"$ref": "#/$defs/general_stats_options"
},
{
"$ref": "#/$defs/ncbi_fcs_options"
},
{
"$ref": "#/$defs/tidk_options"
},
{
"$ref": "#/$defs/busco_options"
},
{
"$ref": "#/$defs/lai_options"
},
{
"$ref": "#/$defs/kraken2_options"
},
{
"$ref": "#/$defs/hic_options"
},
{
"$ref": "#/$defs/merqury_options"
},
{
"$ref": "#/$defs/synteny_options"
},
{
"$ref": "#/$defs/orthofinder_options"
},
{
"$ref": "#/$defs/institutional_config_options"
},
{
"$ref": "#/$defs/generic_options"
}
]
}