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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/IARCbioinfo/alignment-nf/master/nextflow_schema.json",
"title": "IARCbioinfo alignment-nf pipeline parameters",
"description": "This pipeline performs fastq alignment or BAM realignment",
"type": "object",
"definitions": {
"input_output_params": {
"title": "Input_output_params",
"type": "object",
"description": "Input and output parameters",
"default": "",
"properties": {
"input_folder": {
"type": "string",
"description": "Folder containing BAM or fastq files to be aligned"
},
"input_file": {
"type": "string",
"description": "Input file (comma-separated) with 4 columns: SM (sample name), RG (read group ID), pair1 (first fastq of the pair), and pair2 (second fastq of the pair)."
},
"fastq_ext": {
"type": "string",
"description": "Extension of fastq files",
"default": "fastq.gz"
},
"suffix1": {
"type": "string",
"default": "_1",
"description": "Suffix for 1st element of fastq read file pair"
},
"suffix2": {
"type": "string",
"default": "_2",
"description": "Suffix for 2nd element of fastq read file pair"
},
"output_folder": {
"type": "string",
"description": "Output folder for aligned BAMs",
"default": "."
}
}
},
"computing_params": {
"title": "Computing_params",
"type": "object",
"description": "Computing parameters",
"default": "",
"properties": {
"cpu": {
"type": "integer",
"default": 8,
"description": "Number of cpu used by bwa mem and sambamba"
},
"cpu_BQSR": {
"type": "integer",
"description": "Number of CPUs used by GATK BQSR",
"default": 2
},
"mem": {
"type": "integer",
"description": "Size of memory used for alignment (in GB)",
"default": 32
},
"mem_BQSR": {
"type": "integer",
"description": "Size of memory used for GATK BQSR",
"default": 10
}
}
},
"ref_params": {
"title": "Ref_params",
"type": "object",
"description": "Reference parameters",
"default": "",
"properties": {
"ref": {
"type": "string",
"description": "Genome reference fasta file with its index files (.fai, .sa, .bwt, .ann, .amb, .pac, and .dict; in the same directory)",
"default": "hg19.fasta"
},
"bed": {
"type": "string",
"description": "Bed file with interval list"
},
"snp_vcf": {
"type": "string",
"default": "dbsnp.vcf",
"description": "Path to SNP VCF from GATK bundle"
},
"indel_vcf": {
"type": "string",
"default": "Mills_1000G_indels.vcf",
"description": "Path to indel VCF from GATK bundle"
}
}
},
"pipeline_params": {
"title": "Pipeline_params",
"type": "object",
"description": "Pipeline parameters",
"default": "",
"properties": {
"RG": {
"type": "string",
"description": "Samtools read group specification with \"\\t\" between fields (for bwa)",
"default": "PL:ILLUMINA"
},
"postaltjs": {
"type": "string",
"default": "NO_FILE",
"description": "Path to postalignment javascript bwa-postalt.js"
},
"feature_file": {
"type": "string",
"description": "Path to feature file for qualimap",
"default": "NO_FILE"
},
"multiqc_config": {
"type": "string",
"description": "Config yaml file for multiqc",
"default": "NO_FILE"
},
"adapterremoval_opt": {
"type": "string",
"description": "Command line options for AdapterRemoval"
},
"bwa_mem": {
"type": "string",
"description": "bwa-mem command",
"default": "bwa-mem2 mem",
"enum": [
"bwa-mem2 mem",
"bwa mem"
]
},
"trim": {
"type": "boolean",
"description": "Enable adapter sequence trimming"
},
"recalibration": {
"type": "boolean",
"description": "Perform base quality score recalibration (GATK)"
},
"alt": {
"type": "boolean",
"description": "Enable alternative contig handling (for reference genome hg38)"
},
"bwa_option_M": {
"type": "boolean",
"description": "Trigger the -M option in bwa and the corresponding compatibility option in samblaster (marks shorter split hits as secondary)"
},
"help": {
"type": "boolean",
"description": "Display help"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_params"
},
{
"$ref": "#/definitions/computing_params"
},
{
"$ref": "#/definitions/ref_params"
},
{
"$ref": "#/definitions/pipeline_params"
}
]
}