Migrating from yarn to pnpm - ENOENT errors in jest tests

Question

I am trying to migrate a yarn based monorepo to pnpm. For the context, the repo contains a shared folder, which most other projects use. We are using Jest v26 with React v17, and node v20. Trying to migrate from yarn v1.22.4 to pnpm v9.3.0.

I am having problems with jest-based tests. With yarn, everything works smoothly. After migrating to pnpm, with no changes to dependencies at all, I'm getting this error for every test suite:

 FAIL  tests/[redacted].test.ts Test suite failed to run

ENOENT: no such file or directory, open '[redacted - project directory]\node:os'

  at Runtime.readFile (../../node_modules/.pnpm/[email protected][email protected][email protected]_/node_modules/jest-runtime/build/index.js:1987:21)
  at Object.<anonymous> (../../node_modules/.pnpm/@[email protected]/node_modules/@azure/logger/src/log.ts:4:1)
  at Object.<anonymous> (../../node_modules/.pnpm/@[email protected]/node_modules/@azure/logger/src/debug.ts:4:1)
  at Object.<anonymous> (../../node_modules/.pnpm/@[email protected]/node_modules/@azure/logger/src/index.ts:4:1)
  at Object.<anonymous> (../../node_modules/.pnpm/@[email protected]/node_modules/@azure/core-rest-pipeline/src/log.ts:4:1)
  at Object.<anonymous> (../../node_modules/.pnpm/@[email protected]/node_modules/@azure/core-rest-pipeline/src/policies/logPolicy.ts:7:1)
  at Object.<anonymous> (../../node_modules/.pnpm/@[email protected]/node_modules/@azure/core-rest-pipeline/src/createPipelineFromOptions.ts:4:1)
  at Object.<anonymous> (../../node_modules/.pnpm/@[email protected]/node_modules/@azure/core-rest-pipeline/src/index.ts:43:1)
  at Object.<anonymous> (../../node_modules/.pnpm/@[email protected]/node_modules/@azure-rest/core-client/src/restError.ts:4:1)
  at Object.<anonymous> (../../node_modules/.pnpm/@[email protected]/node_modules/@azure-rest/core-client/src/index.ts:9:1)

The *.ts files from the log above do not exist in my filesystem - I have tried opening the exact path from the logs, and I also browsed the node_modules directory. I have no idea where this comes from.

One of the possible solutions I have found on the internet is to migrate to Jest v27 or higher, which indeed solves the issue above. However, v27 comes with breaking changes that breaks a lot of other tests for different reasons.

I have three questions:

1. Why the tests work fine with packages installed via yarn, but fail with packages installed via pnpm?
2. Why are there paths in the logs mentioned above, that do not exist, yet seem to be resolved fine by jest, considering the error stack?
3. Is there any way to resolve this issue, using pnpm but without upgrading jest to v27?

My jest config:

module.exports = {
    preset: "ts-jest",
    setupFilesAfterEnv: ["./tests/setupTests.ts", "./tests/setupMocks.ts"],
    moduleFileExtensions: ["js", "json", "jsx", "ts", "tsx"],
    modulePaths: ["src", "test"],
    moduleDirectories: ["node_modules", "shared"],
    moduleNameMapper: {
        "^.+\\.(css|less|scss)$": "<rootDir>/tests/mocks/styleMock.js",
        "^@ProjectNameMocks(.*)$": "<rootDir>/storybook/stories/mocks$1",
        "^@ProjectNameTests(.*)$": "<rootDir>/tests$1",
        "^@ProjectName(.*)$": "<rootDir>/src$1"
    },
    testEnvironment: "jsdom",
    transform: {
        "^.+\\.(js|jsx)?$": "babel-jest"
    },
    transformIgnorePatterns: ["/node_modules/(?!(\\.pnpm|lodash-es|@fluentui|@azure))"],
    modulePathIgnorePatterns: ["./bin"],
    globals: {
        "ts-jest": {
            tsconfig: "./tsconfig.json"
        }
    }
};