workflows: create separate workflows for GenBank/GISAID ingests

nextstrain · Jun 15, 2020 · acb4e8e · acb4e8e
1 parent 1c743a6
commit acb4e8e
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Showing 4 changed files with 65 additions and 3 deletions.
diff --git a/.github/workflows/ingest-genbank-branch.yml b/.github/workflows/ingest-genbank-branch.yml
@@ -0,0 +1,26 @@
+name: '[branch] Ingest 2019-nCov/SARS-CoV-2 data from GenBank for nextstrain.org/ncov'
+
+on:
+  push:
+    branches-ignore:
+      - master
+    tags-ignore:
+      - '**'
+
+jobs:
+  ingest:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: ingest
+      run: |
+        PATH="$HOME/.local/bin:$PATH"
+        python3 -m pip install --upgrade pip setuptools
+        python3 -m pip install pipenv
+        pipenv sync
+        pipenv run ./bin/ingest-genbank
+      env:
+        AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
+        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        SLACK_TOKEN: ${{ secrets.SLACK_TOKEN }}
diff --git a/.github/workflows/ingest-genbank-master.yml b/.github/workflows/ingest-genbank-master.yml
@@ -0,0 +1,36 @@
+name: Ingest 2019-nCov/SARS-CoV-2 data from GenBank for nextstrain.org/ncov
+
+on:
+  push:
+    branches:
+      - master
+    tags-ignore:
+      - '**'
+    paths:
+      - source-data/genbank_annotations.tsv
+
+  schedule:
+    # See table of scheduled times in the README.  Times here are UTC.
+    - cron: '0 6,12,15,21 * * *'
+
+  # Manually triggered using `./bin/trigger ingest`
+  repository_dispatch:
+    types: ingest
+
+jobs:
+  ingest:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: ingest
+      run: |
+        PATH="$HOME/.local/bin:$PATH"
+        python3 -m pip install --upgrade pip setuptools
+        python3 -m pip install pipenv
+        pipenv sync
+        pipenv run ./bin/ingest-genbank
+      env:
+        AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
+        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        SLACK_TOKEN: ${{ secrets.SLACK_TOKEN }}
diff --git a/.github/workflows/ingest-branch.yml → .github/workflows/ingest-gisaid-branch.yml b/.github/workflows/ingest-branch.yml → .github/workflows/ingest-gisaid-branch.yml
@@ -18,7 +18,7 @@ jobs:
         python3 -m pip install --upgrade pip setuptools
         python3 -m pip install pipenv
         pipenv sync
-        pipenv run ./bin/ingest
+        pipenv run ./bin/ingest-gisaid
       env:
         AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
         AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}

diff --git a/.github/workflows/ingest-master.yml → .github/workflows/ingest-gisaid-master.yml b/.github/workflows/ingest-master.yml → .github/workflows/ingest-gisaid-master.yml
@@ -7,7 +7,7 @@ on:
     tags-ignore:
       - '**'
     paths:
-      - source-data/annotations.tsv
+      - source-data/gisaid_annotations.tsv
 
   schedule:
     # See table of scheduled times in the README.  Times here are UTC.
@@ -28,7 +28,7 @@ jobs:
         python3 -m pip install --upgrade pip setuptools
         python3 -m pip install pipenv
         pipenv sync
-        pipenv run ./bin/ingest
+        pipenv run ./bin/ingest-gisaid
       env:
         AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
         AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}