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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/vmikk/NextITS/main/nextflow_schema.json",
"title": "NextITS pipeline parameters",
"description": "Pipeline to process fungal ITS amplicons sequenced with PacBio",
"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": "path",
"exists": true,
"mimetype": "text/csv",
"description": "Path to the input file containing single-end sequences (in FASTQ format) or the directory with pre-demultiplexed files.",
"fa_icon": "fas fa-file-csv"
},
"barcodes": {
"type": "string",
"fa_icon": "fas fa-barcode",
"description": "Path to the file with barcodes (in FASTA format) used for demultiplexing the input data."
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "Path to the directory where the analysis results will be saved.",
"fa_icon": "fas fa-folder-open"
}
}
},
"demultiplexing": {
"title": "Demultiplexing",
"type": "object",
"description": "",
"default": "",
"properties": {
"demultiplexed": {
"type": "boolean",
"fa_icon": "fas fa-align-justify",
"description": "Whether input is multiplexed (`false`, single FASTQ file) or pre-demultiplexed (`true`, multiple FASTQ files)."
"lima_barcodetype": {
"type": "string",
"default": "dual_symmetric",
"fa_icon": "fab fa-slack-hash",
"description": "Tag type used for multiplexing samples",
"enum": ["single", "dual", "dual_symmetric", "dual_asymmetric"]
},
"lima_minscore": {
"type": "integer",
"default": 93,
"minimum": 0,
"maximum": 100,
"fa_icon": "fas fa-balance-scale-left",
"description": "Barcode score for demultiplexing."
},
},
"lima_W": {
"type": "integer",
"default": 70,
"fa_icon": "fas fa-arrows-alt-h",
"description": "Window size for barcode lookup, in base pairs",
"minimum": 1
},
"lima_minlen": {
"type": "integer",
"default": 40,
"fa_icon": "fas fa-compress-alt",
"description": "Minimum sequence length after clipping barcodes.",
"minimum": 1
},
}
},
"quality_control": {
"title": "Quality Control",
"type": "object",
"description": "Sequence quality filtering",
"default": "",
"properties": {
"qc_maxee": {
"type": "number",
"description": "Maximum number of expected errors.",
"fa_icon": "fas fa-times"
},
"qc_maxeerate": {
"type": "number",
"default": 0.01,
"description": "Maximum number of expected errors per base.",
"fa_icon": "fas fa-times"
},
"qc_maxhomopolymerlen": {
"type": "integer",
"default": 25,
"description": "Threshold for a homopolymer region length in a sequence.",
"fa_icon": "fas fa-redo"
},
"qc_maxn": {
"type": "integer",
"default": 4,
"description": "Discard sequences with more than the specified number of ambiguous nucleotides (N's).",
"fa_icon": "fas fa-minus-square"
}
},
"fa_icon": "fas fa-trash-restore"
},
"primer_trimming": {
"title": "Primer trimming",
"type": "object",
"description": "Removal of primer-artefacts and reorienting of reads",
"default": "",
"properties": {
"primer_forward": {
"type": "string",
"fa_icon": "fas fa-arrow-right",
"description": "Sequence of the forward primer.",
"default": "TACACACCGCCCGTCG",
"help_text": "**Forward Primer:** `ITS9MUNngs` with sequence `TACACACCGCCCGTCG` \nRefer to [Tedersoo & Lindahl, 2016 DOI:`10.1111/1758-2229.12438`](https://ami-journals.onlinelibrary.wiley.com/doi/10.1111/1758-2229.12438) for more details on these primers. "
},
"primer_reverse": {
"type": "string",
"fa_icon": "fas fa-arrow-left",
"description": "Sequence of the reverse primer.",
"default": "CCTSCSCTTANTDATATGC",
"help_text": "**Reverse Primer:** `ITS4ngsUni` with sequence `CCTSCSCTTANTDATATGC` \nRefer to [Tedersoo & Lindahl, 2016 DOI:`10.1111/1758-2229.12438`](https://ami-journals.onlinelibrary.wiley.com/doi/10.1111/1758-2229.12438) for more details on these primers. "
},
"primer_mismatches": {
"type": "integer",
"default": 2,
"fa_icon": "fas fa-chevron-circle-down",
"description": "Allowed number of mismatches for primers."
},
"primer_foverlap": {
"type": "integer",
"fa_icon": "fas fa-angle-right",
"description": "Minimum overlap for the forward primer."
},
"primer_roverlap": {
"type": "integer",
"fa_icon": "fas fa-angle-left",
"description": "Minimum overlap for the reverse primer."
}
},
"fa_icon": "fas fa-crop-alt"
},
"illumina_specific_parameters": {
"title": "Illumina-specific parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"seqplatform": {
"type": "string",
"default": "PacBio",
"fa_icon": "fab fa-google-play"
},
"input_R1": {
"type": "string"
},
"input_R2": {
"type": "string"
},
"qc_avgphred": {
"type": "boolean"
},
"qc_twocolor": {
"type": "boolean"
},
"pe_minoverlap": {
"type": "integer",
"default": 20
},
"pe_diffperclimit": {
"type": "integer",
"default": 20
},
"pe_difflimit": {
"type": "integer",
"default": 5
},
"pe_nlimit": {
"type": "integer",
"default": 10
},
"pe_minlen": {
"type": "integer",
"default": 30
},
"illumina_keep_notmerged": {
"type": "boolean",
"default": true
},
"illumina_joinpadgap": {
"type": "string",
"default": "NNNNNNNNNN"
},
"illumina_joinpadqual": {
"type": "string",
"default": "IIIIIIIIII"
},
"barcode_errors": {
"type": "integer",
"default": 1
},
"barcode_window": {
"type": "integer",
"default": 30
},
"barcode_overlap": {
"type": "integer",
"default": 11
},
"trim_minlen": {
"type": "integer",
"default": 10
},
"qc_phredmin": {
"type": "integer"
},
"qc_phredperc": {
"type": "integer"
},
"qc_polyglen": {
"type": "integer"
}
}
},
"chimera_removal": {
"title": "Chimera removal",
"type": "object",
"description": "",
"default": "",
"properties": {
"chimera_db": {
"type": "string",
"fa_icon": "fas fa-database"
},
"chimera_rescueoccurrence": {
"type": "integer",
"default": 2
},
"chimeranov_abskew": {
"type": "number",
"default": 2
},
"chimeranov_dn": {
"type": "number",
"default": 1.4
},
"chimeranov_mindiffs": {
"type": "number",
"default": 3
},
"chimeranov_mindiv": {
"type": "number",
"default": 0.8
},
"chimeranov_minh": {
"type": "number",
"default": 0.28
},
"chimeranov_xn": {
"type": "number",
"default": 8
}
},
"fa_icon": "fas fa-trash-alt"
},
"tag_jump_removal": {
"title": "Tag-jump removal",
"type": "object",
"description": "",
"default": "",
"properties": {
"tj_f": {
"type": "number",
"default": 0.01,
"minimum": 0,
"maximum": 1
},
"tj_p": {
"type": "number",
"default": 1
},
"otu_id": {
"type": "number",
"default": 0.98,
"minimum": 0,
"maximum": 1
},
"otu_iddef": {
"type": "integer",
"default": 2,
"minimum": 0,
"maximum": 4
}
}
},
"its_extraction": {
"title": "ITS extraction",
"type": "object",
"description": "",
"default": "",
"properties": {
"its_region": {
"type": "string",
"default": "full",
"enum": [
"full",
"ITS1",
"ITS2",
"none",
"ITS1_5.8S_ITS2",
"SSU",
"LSU"
],
"fa_icon": "fas fa-arrows-alt-h"
},
"ITSx_tax": {
"type": "string",
"default": "all",
"fa_icon": "fas fa-user-tag"
},
"ITSx_evalue": {
"type": "number",
"default": 0.1,
"fa_icon": "fas fa-check-circle"
},
"ITSx_partial": {
"type": "integer",
"default": 0,
"fa_icon": "fas fa-arrows-alt-h"
}
}
},
"homopolymer_correction": {
"title": "Homopolymer correction",
"type": "object",
"description": "",
"default": "",
"properties": {
"hp": {
"type": "boolean",
"default": true
},
"hp_similarity": {
"type": "number",
"default": 0.999,
"minimum": 0.8,
"maximum": 1
},
"hp_iddef": {
"type": "number",
"default": 2,
"minimum": 0,
"maximum": 4
}
}
},
"step_2_options": {
"title": "Step 2 options",
"type": "object",
"description": "",
"default": "",
"properties": {
"data_path": {
"type": "string",
"format": "directory-path",
"fa_icon": "fas fa-folder-open",
"description": "Path to the Step-1 results."
}
}
},
"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": {
"storagemode": {
"type": "string",
"default": "rellink",
"fa_icon": "fas fa-boxes",
"enum": ["symlink", "copy", "move", "rellink", "link"],
"description": "Adjusts how files are directed to the results folder."
},
"gzip_compression": {
"type": "number",
"default": 7,
"minimum": 1,
"maximum": 9,
"fa_icon": "fas fa-file-archive",
"description": "Controls GZIP compression level in output files."
},
"help": {
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"helpMsg": {
"type": "boolean",
"fa_icon": "far fa-question-circle"
},
"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})$"
},
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"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
},
"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
},
"tracedir": {
"type": "string",
"default": "results/pipeline_info"
},
"show_hidden_params": {
"type": "boolean",
"description": "Show all params when using `--help`.",
"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.",
"fa_icon": "fas fa-eye-slash"
},
"enable_conda": {
"type": "boolean",
"fa_icon": "fas fa-adjust"
},
"max_cpus": {
"type": "integer",
"default": 8,
"fa_icon": "fas fa-microchip",
"description": "Maximum number of CPUs that can be requested (for any single job).",
"help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`",
"minimum": 1,
"maximum": 200
},
"max_memory": {
"type": "string",
"default": "32.GB",
"fa_icon": "fas fa-memory",
"description": "Maximum amount of memory that can be requested (for any single job).",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
},
"max_time": {
"type": "string",
"default": "240.h",
"fa_icon": "fas fa-clock",
"description": "Maximum amount of time that can be requested (for any single job).",
"pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
"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'`"
},
"schema_ignore_params": {
"type": "string"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/demultiplexing"
},
{
"$ref": "#/definitions/quality_control"
},
{
"$ref": "#/definitions/primer_trimming"
},
{
"$ref": "#/definitions/illumina_specific_parameters"
},
{
"$ref": "#/definitions/chimera_removal"
},
{
"$ref": "#/definitions/tag_jump_removal"
},
{
"$ref": "#/definitions/its_extraction"
},
{
"$ref": "#/definitions/homopolymer_correction"
},
{
"$ref": "#/definitions/step_2_options"
},
{
"$ref": "#/definitions/generic_options"
}
]
}