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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/Zymo-Research/aladdin-smrnaseq/master/nextflow_schema.json",
"title": "Zymo-Research/aladdin-smrnaseq pipeline parameters",
"description": "Nextflow small RNA-Seq analysis pipeline, part of the Zymo research bioinformatics pipeline catalog",
"type": "object",
"definitions": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["design"],
"properties": {
"outdir": {
"type": "string",
"description": "The output directory where the results will be saved.",
"hidden": true,
"default": "./results"
},
"design": {
"type": "string",
"description": "Path to a design CSV file with sample & group labels, and paths to reads files",
"hidden": true
}
}
},
"reference_genome_options": {
"title": "Reference genome options",
"type": "object",
"description": "Options for the reference genome indices used to align reads.",
"properties": {
"genome": {
"type": "string",
"description": "Reference genome used to align reads. Please contact us to add more species.",
"enum": ["Homo_sapiens[GRCh38]", "Rattus_norvegicus[Rnor_6.0]", "Mus_musculus[GRCm38]"]
},
"save_reference": {
"type": "boolean",
"description": "Save reference genome files",
"hidden": true,
"default": false
}
},
"required": ["genome"]
},
"max_job_request_options": {
"title": "Max job request options",
"type": "object",
"description": "Set the top limit for requested resources for any single job.",
"properties": {
"max_cpus": {
"type": "integer",
"description": "Maximum number of CPUs that can be requested for any single job.",
"hidden": true,
"minimum": 1,
"default": 8
},
"max_memory": {
"type": "string",
"description": "Maximum amount of memory that can be requested for any single job.",
"hidden": true,
"default": "60.GB"
},
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job.",
"hidden": true,
"default": "48.h"
}
}
},
"read_trimming_options": {
"title": "Read trimming options",
"type": "object",
"description": "Options to adjust read trimming criteria",
"properties": {
"protocol": {
"type": "string",
"description": "Library prep protocol/kit used. If your kit is not listed, please contact us to request help.",
"enum": ["Zymo-Seq_miRNA"]
},
"trim_nextseq": {
"type": "integer",
"description": "This option will set a new Phred score quality cutoff that will automatically ignore and trim erroneous high quality Gs at the 3' end common on NextSeq or NovaSeq platforms. A value above 0 for this parameter will set a new Phred score. Otherwise, a default Phred score of 20 will be used.",
"advanced": true,
"default": 0,
"minimum": 0,
"maximum": 30
},
"min_length": {
"type": "integer",
"description": "Minimum read length for a read to be kept after trimming",
"advanced": true,
"default": 18,
"minimum": 15,
"maximum": 25
},
"max_length": {
"type": "integer",
"description": "Maximum read length for a read to be kept after trimming. Set max_length to 0 for no maximum read length to be applied.",
"advanced": true,
"default": 0,
"minimum": 0,
"maximum": 2000
},
"save_trimmed": {
"type": "boolean",
"description": "Whether to save FASTQ files post-trimming",
"hidden": true,
"default": false
}
},
"required": ["protocol"]
},
"comparison_options": {
"title": "Differential Expression Analysis Parameters",
"type": "object",
"description": "Options to change differential expression settings for isomiRs and DESeq2",
"properties": {
"isomirs_fdr":{
"type": "number",
"description": "Differential Expression false discovery rate. Sets FDR for both isomiRs and DESeq2.",
"advanced": true,
"minimum": 0,
"maximum": 1,
"default": 0.05
},
"isomirs_lfc":{
"type": "number",
"description": "Differential Expression Log2 Fold Change Threshold. Sets LFC for both isomiRs and DESeq2.",
"advanced": true,
"default": 0.585,
"minimum": 0,
"maximum": 5
},
"comparisons":{
"type":"string",
"description": "Path to a CSV file stating the sample groups you want to compare. If not provided, all pairwise comparisons will be carried out.",
"hidden": true
}
}
},
"process_skipping_options": {
"title": "Process skipping options",
"type": "object",
"description": "Options to skip various steps in the workflow",
"properties": {
"skip_fastqc": {
"type": "boolean",
"description": "Skip FASTQC step",
"hidden": true,
"default": false
},
"skip_multiqc": {
"type": "boolean",
"description": "Skip MultiQC step",
"hidden": true,
"default": false
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"description": "Less common options for the pipeline, typically set in a config file.",
"properties": {
"name": {
"type": "string",
"description": "Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic",
"hidden": true
},
"help": {
"type": "boolean",
"description": "Whether to display help message",
"hidden": true,
"default": false
},
"tracedir": {
"type": "string",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"hidden": true,
"default": "${params.outdir}/pipeline_info"
},
"awsqueue": {
"type": "string",
"description": "AWS Batch queue to submit jobs to",
"hidden": true
},
"awsregion": {
"type": "string",
"description": "AWS region",
"hidden": true,
"default": "us-east-1"
},
"profile": {
"type": "string",
"description": "Run the pipeline on a specific compute environment.",
"hidden": true,
"default": "awsbatch"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/reference_genome_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/read_trimming_options"
},
{
"$ref": "#/definitions/comparison_options"
},
{
"$ref": "#/definitions/process_skipping_options"
},
{
"$ref": "#/definitions/generic_options"
}
]
}