package.json

{
  "name": "bionode-example-dat-gasket",
  "version": "1.0.0",
  "description": "",
  "main": "index.js",
  "scripts": {
    "init": "dat init --no-prompt",
    "fetch": "gasket run fetch-eukaryota-genomes-metadata",
    "search": "gasket run search-ncbi-metadata",
    "align": "gasket run index-and-align",
    "bam": "gasket run convert-to-bam"
  },
  "dependencies": {
    "bionode-bwa": "0.0.9",
    "bionode-ncbi": "^1.0.1",
    "bionode-sam": "^1.0.1",
    "bionode-sra": "^1.0.0",
    "dat": "^6.8.1",
    "gasket": "^1.3.0",
    "tool-stream": "^0.2.1"
  },
  "author": {
    "name": "Bruno Vieira",
    "email": "mail@bmpvieira.com"
  },
  "license": "MIT",
  "gasket": {
    "fetch-eukaryota-genomes-metadata": [
      "bionode-ncbi search genome eukaryota",
      "dat import --json --primary=uid"
    ],
    "search-ncbi-metadata": [
      "dat cat",
      "grep Guillardia",
      "tool-stream extractProperty assemblyid",
      "bionode-ncbi download assembly -",
      "tool-stream collectMatch status completed",
      "tool-stream extractProperty uid",
      "bionode-ncbi link assembly bioproject -",
      "tool-stream extractProperty destUID",
      "bionode-ncbi link bioproject sra -",
      "tool-stream extractProperty destUID",
      "grep 35526",
      "bionode-ncbi download sra -",
      "tool-stream collectMatch status completed",
      "tee > metadata.json"
    ],
    "index-and-align": [
      "cat metadata.json",
      "bionode-sra fastq-dump -",
      "tool-stream extractProperty destFile",
      "bionode-bwa mem **/*fna.gz"
    ],
    "convert-to-bam": [
      "bionode-sam 35526/SRR070675.sam"
    ]
  }
}