nextflow_schema.json

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/bostongene/pyigmap/main/nextflow_schema.json",
  "title": "bostongene/pyigmap pipeline parameters",
  "description": "A pipeline for extracting and summarizing TCR and BCR gene rearrangements from sequencing data",
  "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": ["outdir"],
      "properties": {
        "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"
        }
      }
    },
    "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",
          "hidden": true
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/input_output_options"
    },
    {
      "$ref": "#/definitions/generic_options"
    }
  ],
  "properties": {
    "fq1": {
      "type": "string"
    },
    "fq2": {
      "type": "string"
    },
    "sample_id": {
      "type": "string",
      "default": "sample"
    },
    "library": {
      "type": "string"
    },
    "mock_merge_amplicon": {
      "type": "boolean"
    },
    "fq1_pattern": {
      "type": "string"
    },
    "fq2_pattern": {
      "type": "string"
    },
    "out_pyumi_fq1": {
      "type": "string",
      "default": "pR1.fastq.gz"
    },
    "out_pyumi_fq2": {
      "type": "string",
      "default": "pR2.fastq.gz"
    },
    "out_pyumi_json": {
      "type": "string",
      "default": "pyumi.json"
    },
    "out_calib_dedup_fq1": {
      "type": "string",
      "default": "cR1.fastq.gz"
    },
    "out_calib_dedup_fq2": {
      "type": "string",
      "default": "cR2.fastq.gz"
    },
    "kmer_size": {
      "type": "integer",
      "default": 4
    },
    "minimizer_count": {
      "type": "integer",
      "default": 7
    },
    "minimizer_threshold": {
      "type": "integer",
      "default": 3
    },
    "error_tolerance": {
      "type": "integer",
      "default": 2
    },
    "out_fastp_fq1": {
      "type": "string",
      "default": "mR1.fastq.gz"
    },
    "out_fastp_fq2": {
      "type": "string",
      "default": "mR2.fastq.gz"
    },
    "out_fastp_fq12": {
      "type": "string",
      "default": "mR12.fastq.gz"
    },
    "out_fastp_json": {
      "type": "string",
      "default": "fastp.json"
    },
    "out_fastp_html": {
      "type": "string",
      "default": "fastp.html"
    },
    "insert_size": {
      "type": "integer",
      "default": 1
    },
    "disable": {
      "type": "string",
      "default": "length_filtering quality_filtering"
    },
    "vidjil_ref": {
      "type": "string",
      "default": "./bin/vidjil/vidjil.germline.tar.gz"
    },
    "out_vidjil_fasta": {
      "type": "string",
      "default": "vidjil.fasta.gz"
    },
    "out_vidjil_logs": {
      "type": "string",
      "default": "vidjil.log"
    },
    "igblast_receptor": {
      "type": "string",
      "default": "all"
    },
    "igblast_organism": {
      "type": "string",
      "default": "human"
    },
    "all_alleles": {
      "type": "boolean"
    },
    "out_igblast_annotation": {
      "type": "string",
      "default": "raw_annotation.tsv.gz"
    },
    "igblast_ref": {
      "type": "string",
      "default": "./bin/igblast/igblast.reference.major_allele.tar.gz"
    },
    "olga_models": {
      "type": "string",
      "default": "./bin/cdr3nt_error_corrector/olga-models.tar.gz"
    },
    "out_corrected_annotation": {
      "type": "string",
      "default": "corrected_annotation.tsv"
    },
    "out_stat_json": {
      "type": "string",
      "default": "stat.json"
    },
    "out_archive": {
      "type": "string",
      "default": "pyigmap.tar.gz"
    },
    "default_corrector_options": {
      "type": "string",
      "default": "--error-rate 0.001 --discard-junctions-with-n --only-best-alignment --remove-chimeras"
    },
    "rnaseq_corrector_options": {
      "type": "string",
      "default": "--filter-pgen-singletons 0 --top-c-call --top-v-alignment-call"
    },
    "amplicon_corrector_options": {
      "type": "string",
      "default": "--skip-pgen-calculation"
    },
    "save_all": {
      "type": "boolean"
    },
    "min_reads_per_cluster": {
      "type": "integer",
      "default": 1
    },
    "max_reads_per_cluster": {
      "type": "integer",
      "default": 50000
    },
    "first_reads": {
      "type": "string",
      "default": "all"
    }
  }
}