main.yml

name: Monitoring Norwegian submissions to SRA samples

on:
  schedule:
    - cron: "0 0 * * *"
  workflow_dispatch:      

jobs:
  default-shell:
    name: Default shell
    runs-on: "ubuntu-latest"
    permissions:
      contents: write
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - uses: actions/checkout@master
        with:
          persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
          fetch-depth: 0             # otherwise, you will fail to push refs to dest repo      - uses: conda-incubator/setup-miniconda@v3
      - uses: conda-incubator/setup-miniconda@v3
        with:
          activate-environment: EBIsearch
          environment-file: EBIsearch_environment.yml
      - run: | 
          python monitoring_sra-samples_EBIsearch.py
      - name: Commit & Push changes
        uses: actions-js/push@master
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          message: "Automated commit"