working-directory を指定すればOK。

jobs:
  job1:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash
        working-directory: ./scripts

ref. Workflow syntax for GitHub Actions - GitHub Docs

name: CI

on: [push]

jobs:
  phpunit:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v1
      - name: Setup Symfony
        working-directory: ./app
        run: cp .env.dev .env
      - name: Install Composer Dependencies
        working-directory: ./app
        run: composer install --prefer-dist
      - name: Run Tests
        working-directory: ./app
        run: php bin/phpunit

ref. github - Running actions in another directory - Stack Overflow