pathogen-repo-build: Support assuming an AWS role via GitHub Actions'…

… OIDC provider

The default role has a pretty limited set of permissions right now:
basically only those required to submit and interact with AWS Batch
jobs, but not, for example, permissions to upload to our production S3
buckets.  The permissions will probably need to be extended in the
future as repos/builds opt into this workflow and this role assumption.
The role's trust policy will also need to be extended to allow other
repos to assume it.

While the role is currently manually managed, it should really be
managed by a Terraform configuration (but maybe one separate from the
current nextstrain.org Terraform configurations?).

Related-to: <nextstrain/private#22>

.github/workflows/pathogen-repo-build.yaml

@@ -29,13 +29,20 @@ on:
           Currently only supports docker, conda, and aws-batch.
           Defaults to "docker".
 
-          The aws-batch runtime requires the secrets:
+          The aws-batch runtime requires AWS credentials.  These may come
+          directly from secrets or indirectly from assuming a role via GitHub
+          Actions' OIDC provider.
+
+          The following secrets are used if present:
 
           - AWS_ACCESS_KEY_ID
           - AWS_SECRET_ACCESS_KEY
 
           They must be defined in the repo's Actions secrets and passed to this
           workflow with `secrets: inherit`.
+
+          If no secrets are present, the GitHubActionsRoleNextstrainBatchJobs
+          role is assumed (in both senses of the verb).
         type: string
         default: docker
         required: false
@@ -57,7 +64,13 @@ on:
 
           All environment variables provided via the env input and all secrets
           provided via `secrets: inherit` can be passed to the build runtime
-          via the `--env` option.
+          via the `--env` option.  If AWS credentials were acquired by the
+          GitHub Action job via role assumption, the following environment
+          variables are also available to be passed:
+
+            - AWS_ACCESS_KEY_ID
+            - AWS_SECRET_ACCESS_KEY
+            - AWS_SESSION_TOKEN
         type: string
         default: nextstrain build .
         required: false
@@ -136,11 +149,12 @@ on:
 env:
   NEXTSTRAIN_GITHUB_DIR: .git/nextstrain/.github
 
+permissions:
+  id-token: write
+
 jobs:
   workflow-context:
     runs-on: ubuntu-latest
-    permissions:
-      id-token: write
     steps:
       - id: workflow-context
         uses: nextstrain/.github/actions/workflow-context@master
@@ -167,16 +181,6 @@ jobs:
           ref: ${{ needs.workflow-context.outputs.sha }}
           path: ${{ env.NEXTSTRAIN_GITHUB_DIR }}
 
-      - name: Setup runtime ${{ inputs.runtime }}
-        uses: ./.git/nextstrain/.github/actions/setup-nextstrain-cli
-        with:
-          cli-version: ">=7.1.0"
-          runtime: ${{ inputs.runtime }}
-        # Required to set up aws-batch as default runtime
-        env:
-          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-
       - if: inputs.env
         name: Set environment variables
         env:
@@ -199,6 +203,21 @@ jobs:
           | "$NEXTSTRAIN_GITHUB_DIR"/bin/json-to-envvars
           | tee -a "$GITHUB_ENV"
 
+      - if: inputs.runtime == 'aws-batch'
+        uses: aws-actions/configure-aws-credentials@v2
+        with:
+          aws-region: us-east-1
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          role-to-assume: ${{ secrets.AWS_ACCESS_KEY_ID == '' && 'arn:aws:iam::827581582529:role/GitHubActionsRoleNextstrainBatchJobs' || '' }}
+          credential-lifetime: 43200 # seconds, or 12 hours
+
+      - name: Setup runtime ${{ inputs.runtime }}
+        uses: ./.git/nextstrain/.github/actions/setup-nextstrain-cli
+        with:
+          cli-version: ">=7.1.0"
+          runtime: ${{ inputs.runtime }}
+
       - name: Run build via ${{ inputs.runtime }}
         env:
           NEXTSTRAIN_BUILD_COMMAND: ${{ inputs.run }}