Merge pull request #76 from nextstrain/refactor-workflow

Refactor workflow

.github/workflows/ci.yaml

@@ -8,4 +8,4 @@ jobs:
   ci:
     uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master
     with:
-      build-args: auspice/flu_seasonal_h3n2_ha_12y.json auspice/flu_seasonal_h3n2_ha_12y_tip-frequencies.json
+      build-args: --configfile profiles/ci/builds.yaml -p

.github/workflows/upload.yaml

@@ -0,0 +1,32 @@
+name: Upload data from fauna to S3
+
+# Only support manual trigger of this workflow.
+on: workflow_dispatch
+
+jobs:
+  upload:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: refactor-workflow
+      # Install Nextstrain CLI, so we can run the flu workflow.
+      - uses: nextstrain/.github/actions/setup-nextstrain-cli@master
+      # Run the flu workflow that downloads titers and sequences from fauna and
+      # uploads to S3.
+      - name: Download from fauna and upload to S3
+        run: |
+          set -x
+
+          nextstrain build \
+            --docker \
+            . \
+            -j 4 \
+            upload_all_titers \
+            upload_all_sequences \
+            --configfile profiles/upload.yaml
+        env:
+          RETHINK_HOST: ${{ secrets.RETHINK_HOST }}
+          RETHINK_AUTH_KEY: ${{ secrets.RETHINK_AUTH_KEY }}
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}

.gitignore

@@ -1,9 +1,11 @@
 # Files created by the pipeline, which we want to keep out of git
 # (or at least out of _this_ git repo).
 data/
+builds/
 results/
 auspice/
 auspice-who/
+auspice_renamed/
 build/
 logs/
 figures/
@@ -51,3 +53,7 @@ nohup.out
 
 # cluster logs
 slurm-*
+
+# Jupyter/Altair droppings
+.ipynb_checkpoints
+geckodriver.log