diff --git a/.github/workflows/phylogenetic-fauna.yaml b/.github/workflows/phylogenetic-fauna.yaml index 2abff69..a0851d5 100644 --- a/.github/workflows/phylogenetic-fauna.yaml +++ b/.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