Script to merge multiple nyc/istanbul code coverage json reports into a single html report: http://rundef.com/typescript-code-coverage-istanbul-nyc

merge-nyc-code-coverage-reports.js

var path = require('path'),
  fs = require('fs'),
  libCoverage = require('nyc/node_modules/istanbul-lib-coverage'),
  libReport = require('nyc/node_modules/istanbul-lib-report'),
  reports = require('nyc/node_modules/istanbul-reports');

var rootFolder = __dirname;
var mergeIntoFolder = 'final';
var files = fs.readdirSync(rootFolder);
var mergedCoverageMap = null;

for(var i = 0; i < files.length; i++) {
  var fullPath = path.resolve(rootFolder, files[i]);

  if(files[i] !== mergeIntoFolder && fs.statSync(fullPath).isDirectory()) {
    fullPath = path.resolve(fullPath, 'coverage-final.json');

    var map = libCoverage.createCoverageMap(JSON.parse(fs.readFileSync(fullPath, 'utf8')));
    if (mergedCoverageMap !== null) {
      mergedCoverageMap.merge(map);
    }
    else {
      mergedCoverageMap = map;
    }
  }
}

var context = libReport.createContext({
  dir: path.join(rootFolder, mergeIntoFolder)
});

tree = libReport.summarizers.pkg(mergedCoverageMap);

tree.visit(reports.create('html'), context);

fs.writeFileSync(path.join(rootFolder, '..', '..', '.nyc_output', 'coverage-final.json'), JSON.stringify(mergedCoverageMap.toJSON()));

This was a great help for recursively generating coverage reports using nyc and mocha programmatically. Thank you!

@supnate - you could also use the --temp-directory flag, wich lets you specify where the output is written.

You can also just use nyc --no-clean to prevent it from clearing out .nyc_output