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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/./master/nextflow_schema.json",
"title": ". pipeline parameters",
"description": "Synteny analysis",
"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", "database", "FW_primer", "RV_primer"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"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"
},
"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"
},
"database": {
"type": "string",
"description": "Path to database fasta file to be used in vsearch sintax module."
},
"single_end": {
"type": "boolean",
"description": "Tells pipeline whether to expect single end or paired-end data."
},
"FW_primer": {
"type": "string",
"description": "Sequence of the forward primer."
},
"RV_primer": {
"type": "string",
"description": "Sequence of the reverse primer."
},
"custom_config": {
"type": "string",
"description": "A path to a custom configuration file."
}
}
},
"module_options": {
"title": "Module options",
"type": "object",
"description": "Additional options provided to module commands",
"default": "",
"properties": {
"cutadapt_min_overlap": {
"type": "integer",
"default": 3,
"description": "Cutadapt module minimum overlap parameter."
},
"cutadapt_max_error_rate": {
"type": "number",
"default": 0.1,
"description": "Cutadapt module max error rate parameter."
},
"pacbio": {
"type": "boolean",
"description": "Cutadapt module pacbio parameter."
},
"iontorrent": {
"type": "boolean",
"description": "Cutadapt module iontorrent parameter."
},
"pear_p_value": {
"type": "integer",
"description": "Pear p-value parameter."
},
"pear_min_overlap": {
"type": "integer",
"description": "Pear min overlap parameter."
},
"pear_max_len": {
"type": "integer",
"description": "Pear max length parameter."
},
"pear_min_len": {
"type": "integer",
"description": "Pear min length parameter."
},
"pear_trimmed_min_len": {
"type": "integer",
"description": "Pear trimmed min length parameter."
},
"pear_quality": {
"type": "integer",
"description": "Pear quality score threshold parameter."
},
"pear_max_uncalled": {
"type": "integer",
"description": "Pear percentage max uncalled parameter."
},
"pear_stat_test": {
"type": "integer",
"description": "Pear statistical test parameter (1 or 2 - check their docs for details)."
},
"pear_scoring_method": {
"type": "integer",
"description": "Pear scoring method parameter (1,2 or 3 - check their docs for details)."
},
"pear_phred": {
"type": "integer",
"description": "Pear phred score threshold parameter."
},
"fastq_maxee": {
"type": "number",
"description": "vsearch fastq max expected errors parameter."
},
"fastq_minlen": {
"type": "integer",
"description": "vsearch fastq min length parameter."
},
"fastq_maxns": {
"type": "integer",
"description": "vsearch max Ns parameter."
},
"fasta_width": {
"type": "integer",
"description": "vsearch fasta width parameter."
},
"minuniquesize": {
"type": "integer",
"description": "vsearch min unique size parameter.",
"default": 2
},
"derep_strand": {
"type": "string",
"description": "vsearch fastq dereplicate strand parameter."
},
"sintax_cutoff": {
"type": "number",
"description": "vsearch sintax cutoff parameter."
},
"sintax_strand": {
"type": "string",
"description": "vsearch sintax strand parameter."
},
"clean": {
"type": "boolean",
"default": false,
"description": "Enable cleanup function."
},
"seed": {
"type": "number",
"description": "vsearch sinxtax random seed parameter.",
"default": 1312
},
"ncbi_settings": {
"type": "string",
"description": "Path to ncbi_settings folder"
},
"certificate": {
"type": "string",
"description": "Path to certificate file"
}
}
},
"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"
},
"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"]
},
"forks": {
"type": "number",
"description": "Maximum number of each process that will be run in parallel."
},
"gitpod": {
"type": "boolean",
"description": "Skips usearch process, which does not run on gitpod (32bit)"
}
}
},
"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",
"help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
},
"max_memory": {
"type": "string",
"description": "Maximum amount of memory that can be requested for any single job.",
"default": "128.GB",
"fa_icon": "fas fa-memory",
"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",
"description": "Maximum amount of time that can be requested for any single job.",
"default": "48.h",
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
"help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
}
}
},
"amazon_options": {
"title": "Amazon Options",
"type": "object",
"description": "AWS batch options",
"default": "",
"properties": {
"awsqueue": {
"type": "string",
"description": "aws queue to use with aws batch",
"default": "HUNDRED_QUEUE"
},
"awsregion": {
"type": "string",
"default": "us-east-1",
"description": "aws region to use with aws batch"
},
"awscli": {
"type": "string",
"description": "path to aws cli installation on host instance",
"default": "/home/ec2-user/miniconda/bin/aws"
},
"s3bucket": {
"type": "string",
"description": "s3 bucket path to use as work directory",
"default": "s3://nextflow-programmatic/test_env/"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/module_options"
},
{
"$ref": "#/definitions/generic_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/amazon_options"
}
]
}