ST_transcriptomics/nextflow_schema.json at main · francops1722/ST_transcriptomics · GitHub

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{
  "type": "object",
  "properties": {
    "UMItype": {
      "type": "string",
      "description":"UMI can be random or semi",
      "default": "random"
    },
    "flavour": {
      "type": "string",
      "description":"Pipeline to run: ST, QSP",
      "default": "ST"
    },
    "genome": {
      "type": "string",
      "description":"add the path to the reference genome",
      "default": "/data/gent/vo/000/gvo00027/resources/STAR_index/Homo_sapiens/GRCh38.dna.primary_assembly.chrIS_spikes_45S.star_index"
    },
    "gtf_file": {
      "type": "string",
      "description":"add the path to the gtf file",
      "default": "/data/gent/vo/000/gvo00027/resources/Ensembl_transcriptomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.109.chrIS_spikes_45S.gtf"
    },
    "CSVfile": {
      "type": "string",
      "description":"add the path to the samplesheet",
      "default": "/kyukon/scratch/gent/vo/000/gvo00027/vsc44685/ST_transcriptomics_local/testing/Test_CSV.csv"
    },
    "reads": {
      "type": "string",
      "description":"path to the fastqfiles"
    },
    "outdir": {
      "type": "string",
      "description":"add the path to save the outputs",
      "default": "/user/gent/446/vsc44685/ScratchVO_dir/Adv_NF_2"
    },
    "Subs": {
      "type": "integer",
      "description":"Number of reads to downsample all files",
      "default": 10000
    },
    "N42": {
      "type": "integer",
      "description":"levenshtein distance threshold for barcode decoding",
      "default": 10
    },
    "N21": {
      "type": "integer",
      "description":"levenshtein distance threshold for barcode decoding",
      "default": 11
    },
    "N3": {
      "type": "integer",
      "description":"levenshtein distance threshold for barcode decoding",
      "default": 12
    },
    "M": {
      "type": "integer",
      "description":"length of barcode",
      "default": 36
    },
    "Ntriage": {
      "type": "integer",
      "description":"Number of barcodes to pass triage",
      "default": 100
    }
  },
  "required": ["CSVfile", "UMItype", "genome", "gtf_file", "Ntriage"]
}