map_to_genbank_seqs.yml

name: Map to GenBank Sequences
run-name: ${{ github.event.inputs.reason || 'Scheduled Run' }}
on:
  schedule:
    - cron: '0 18 * * *'
  workflow_dispatch:
    inputs:
      reason:
        description: 'Reason for running the workflow'
        required: true
        default: 'Routine Processing'

concurrency:
  group: ${{ github.repository }}

jobs:
  map_to_genbank_seqs:
    runs-on: ubuntu-22.04
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - name: Checkout code
        uses: actions/checkout@v4
      - name: Map to GenBank Sequences
        run: bash scripts/map_genbank.sh ${{ github.workspace }}/metadata/SraRunTable_automated.csv ${{ github.workspace }}/fasta/ > ${{ github.workspace }}/genbank_mapping.tsv
      - name: Push GenBank Mappings
        run: |
          git config --global user.email "github-actions[bot]@users.noreply.github.com"
          git config --global user.name "github-actions[bot]"
          mv ${{ github.workspace }}/genbank_mapping.tsv ${{ github.workspace }}/metadata/genbank_mapping.tsv
          if [[ $(git status --porcelain ${{ github.workspace }}/metadata/genbank_mapping.tsv) ]]; then
            git add ${{ github.workspace }}/metadata/genbank_mapping.tsv
            git commit -m "Update GenBank mappings"
            git push
          fi