adds auto-updating

.github/workflows/pull_data.yml

@@ -0,0 +1,46 @@
+# This workflow will install pytest, and test validity of data in repo.
+
+name: Data integration
+
+on:
+  push:
+    branches: [ "main" ]
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.NICD_TOKEN }}
+
+      - name: Checkout private tools
+        uses: actions/checkout@v3
+        with:
+          repository: NICD-Wastewater-Genomics/NICD-Freyja-outputs-
+          token: ${{ secrets.NICD_TOKEN }}
+          path: NICD-Freyja-outputs-
+
+      - name: Clone 
+        shell: bash -l {0}
+        run: |
+            git config --global user.name "joshuailevy"
+            git config --global user.email "joshua.levy16@gmail.com"
+            cp NICD-Freyja-outputs-/scripts/NICD_daily_smoothed.csv Dashboard/data/
+            cp NICD-Freyja-outputs-/scripts/NICD_monthly.csv Dashboard/data/
+            cp NICD-Freyja-outputs-/scripts/color_map.json Dashboard/data/
+            cp NICD-Freyja-outputs-/scripts/merged_data.tsv Dashboard/data/
+    
+      - name: Push
+        run: |
+          if [[($(git status Dashboard/data/merged_data.tsv --porcelain | wc -c) -ne 0)]]; then
+            git add --all
+            git commit -m "automated core data update"
+            git push origin main
+          else
+            echo "no new samples, nothing to do"
+          fi