RNAseq-nextflow/nextflow_schema.json at main · aledavini7/RNAseq-nextflow · GitHub

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{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com///nextflow_schema.json",
  "title": "Pipeline parameters",
  "description": "",
  "type": "object",
  "properties": {
    "reads": {
      "type": "string",
      "format": "file-path",
      "description": "FASTQ reads from RNA-seq experiment",
      "help_text": ""
    },
    "bams": {
      "type": "string",
      "format": "file-path",
      "description": "Aligned reads obtained after mapping"
    },
    "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"
    },
    "gtf_rnaseq": {
      "type": "string",
      "format": "file-path",
      "default": "/hpcnfs/scratch/ED/genome/GRCh38_human_v39/gencode.v39.primary_assembly.annotation.gtf",
      "description": "Genome reference file"
    },
    "gtf_bed_strandness": {
      "type": "string",
      "format": "file-path",
      "default": "/hpcnfs/scratch/ED/genome/GRCh38_human_v39/gencode.v39.primary_assembly.annotation.gtf.bed",
      "description": "Genome reference BED file"
    },
    "index": {
      "type": "string",
      "format": "directory-path",
      "default": "/hpcnfs/scratch/ED/genome/GRCh38_human_v39/STAR",
      "description": "Genome reference index directory"
    },
    "run_strandness": {
      "type": "boolean",
      "description": "Optional workflow to infer strandness of reads",
      "default": false
    }
  },
  "required": ["outdir"]
}