wip

.github/workflows/phylogenetic-fauna.yaml

@@ -25,33 +25,77 @@ on:
         type: string
 
 jobs:
-  phylogenetic:
-    permissions:
-      id-token: write
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
-    secrets: inherit
-    with:
-      runtime: aws-batch
-      run: |
-        declare -a config;
-
-        if [[ "$TRIAL_NAME" ]]; then
-          config+=(
-            deploy_url="s3://nextstrain-staging/avian-flu_trials_${TRIAL_NAME}_"
-          )
-        fi;
-
-        nextstrain build \
-          --detach \
-          --no-download \
-          --cpus 16 \
-          --memory 28800mib \
-          . \
-            deploy_all \
-            --configfile config/gisaid.yaml \
-            --config "${config[@]}"
-
-      env: |
-        NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
-        TRIAL_NAME: ${{ inputs.trial-name }}
-      artifact-name: phylogenetic-fauna-build-output
+  summary:
+    runs-on: ubuntu-latest
+    steps:
+      - name: summary_step
+        run: |
+          # Print a summary of the URLs where you can view the results of this run
+          URL_A="avian-flu/h5n1/ha/2y"
+          URL_B="avian-flu/h9n2/pb2/all-time"
+          if [[ "$TRIAL_NAME" ]]; then
+              echo "## Trial Build URLs" >> $GITHUB_STEP_SUMMARY
+
+              URL_START="https://nextstrain.org/staging/avian-flu/trials"
+              TRIAL_NAME_URL=$( echo "$TRIAL_NAME" | sed "s|_|/|g" )
+
+              echo "" >> $GITHUB_STEP_SUMMARY
+              echo "  * ${URL_START}/${TRIAL_NAME_URL}/${URL_A}" >> $GITHUB_STEP_SUMMARY
+              echo "  * ${URL_START}/${TRIAL_NAME_URL}/${URL_B}" >> $GITHUB_STEP_SUMMARY
+              echo -e "\netc\n" >> $GITHUB_STEP_SUMMARY
+          else
+              echo "## Canonical URLs will be updated by this run" >> $GITHUB_STEP_SUMMARY
+              URL_START="https://nextstrain.org"
+              echo "" >> $GITHUB_STEP_SUMMARY
+              echo "  * ${URL_START}/${URL_A}" >> $GITHUB_STEP_SUMMARY
+              echo "  * ${URL_START}/${URL_B}" >> $GITHUB_STEP_SUMMARY
+              echo -e "\netc\n" >> $GITHUB_STEP_SUMMARY
+
+          fi;
+          echo "> NOTE: These URL paths may be incorrect if you've changed the  " >> $GITHUB_STEP_SUMMARY
+          echo "> snakemake targets in 'config/gisaid.yaml' as part of this PR." >> $GITHUB_STEP_SUMMARY
+          echo "> Please update this GitHub Action if so!" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "## Docker container used for this run" >> $GITHUB_STEP_SUMMARY
+          if [[ "$NEXTSTRAIN_DOCKER_IMAGE" ]]; then
+              echo "Docker image: $NEXTSTRAIN_DOCKER_IMAGE" >> $GITHUB_STEP_SUMMARY
+          else
+              echo "Docker image: default (latest)" >> $GITHUB_STEP_SUMMARY
+          fi;echo "## Docker container used for this run" >> $GITHUB_STEP_SUMMARY
+
+          echo "## Git Branch" >> $GITHUB_STEP_SUMMARY
+          echo "  * ${BRANCH_NAME}" >> $GITHUB_STEP_SUMMARY
+    env:
+      NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
+      TRIAL_NAME: ${{ inputs.trial-name }}
+      BRANCH_NAME: ${{ github.head_ref || github.ref_name }} 
+  # phylogenetic:
+  #   permissions:
+  #     id-token: write
+  #   uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+  #   secrets: inherit
+  #   with:
+  #     runtime: aws-batch
+  #     run: |
+  #       declare -a config;
+
+  #       if [[ "$TRIAL_NAME" ]]; then
+  #         config+=(
+  #           deploy_url="s3://nextstrain-staging/avian-flu_trials_${TRIAL_NAME}_"
+  #         )
+  #       fi;
+
+  #       nextstrain build \
+  #         --detach \
+  #         --no-download \
+  #         --cpus 16 \
+  #         --memory 28800mib \
+  #         . \
+  #           deploy_all \
+  #           --configfile config/gisaid.yaml \
+  #           --config "${config[@]}"
+
+  #     env: |
+  #       NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
+  #       TRIAL_NAME: ${{ inputs.trial-name }}
+  #     artifact-name: phylogenetic-fauna-build-output