diff --git a/.github/workflows/phylogenetic-fauna.yaml b/.github/workflows/phylogenetic-fauna.yaml index 2abff69..169af21 100644 --- a/.github/workflows/phylogenetic-fauna.yaml +++ b/.github/workflows/phylogenetic-fauna.yaml @@ -25,6 +25,46 @@ on: type: string jobs: + summary: + runs-on: ubuntu-latest + steps: + - name: summary_step + run: | + URL_A="avian-flu/h5n1/ha/2y" + URL_B="avian-flu/h9n2/pb2/all-time" + if [[ "$TRIAL_NAME" ]]; then + echo "### Trial Build URLs" >> $GITHUB_STEP_SUMMARY + URL_BASE="https://nextstrain.org/staging/avian-flu/trials" + TRIAL_NAME_URL=$( echo "$TRIAL_NAME" | sed "s|_|/|g" ) + echo "" >> $GITHUB_STEP_SUMMARY + echo " * ${URL_BASE}/${TRIAL_NAME_URL}/${URL_A}" >> $GITHUB_STEP_SUMMARY + echo " * ${URL_BASE}/${TRIAL_NAME_URL}/${URL_B}" >> $GITHUB_STEP_SUMMARY + echo " * etc" >> $GITHUB_STEP_SUMMARY + else + echo "### Canonical URLs will be updated by this run" >> $GITHUB_STEP_SUMMARY + URL_BASE="https://nextstrain.org" + echo "" >> $GITHUB_STEP_SUMMARY + echo " * ${URL_BASE}/${URL_A}" >> $GITHUB_STEP_SUMMARY + echo " * ${URL_BASE}/${URL_B}" >> $GITHUB_STEP_SUMMARY + echo " * etc" >> $GITHUB_STEP_SUMMARY + fi; + echo "" >> $GITHUB_STEP_SUMMARY + NOTE="NOTE: These URL paths may be incorrect if you've changed the " + NOTE+="snakemake targets in 'config/gisaid.yaml' as part of this PR. " + NOTE+="Please update this GitHub Action if so!" + echo "> $NOTE" >> $GITHUB_STEP_SUMMARY + echo "" >> $GITHUB_STEP_SUMMARY + echo "### Build (meta-)environment" >> $GITHUB_STEP_SUMMARY + if [[ "$NEXTSTRAIN_DOCKER_IMAGE" ]]; then + echo " * Docker image: $NEXTSTRAIN_DOCKER_IMAGE" >> $GITHUB_STEP_SUMMARY + else + echo " * Docker image: default (latest)" >> $GITHUB_STEP_SUMMARY + fi; + echo " * Git Branch: `${BRANCH_NAME}`" >> $GITHUB_STEP_SUMMARY + env: + NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }} + TRIAL_NAME: ${{ inputs.trial-name }} + BRANCH_NAME: ${{ github.head_ref || github.ref_name }} phylogenetic: permissions: id-token: write diff --git a/.github/workflows/phylogenetic-ncbi.yaml b/.github/workflows/phylogenetic-ncbi.yaml index 096e0f1..da48073 100644 --- a/.github/workflows/phylogenetic-ncbi.yaml +++ b/.github/workflows/phylogenetic-ncbi.yaml @@ -32,6 +32,46 @@ on: type: string jobs: + summary: + runs-on: ubuntu-latest + steps: + - name: summary_step + run: | + URL_A="avian-flu/h5n1-cattle-outbreak/genome" + URL_B="avian-flu/h5n1-cattle-outbreak/ha" + if [[ "$TRIAL_NAME" ]]; then + echo "### Trial Build URLs" >> $GITHUB_STEP_SUMMARY + URL_BASE="https://nextstrain.org/staging/avian-flu/trials" + TRIAL_NAME_URL=$( echo "$TRIAL_NAME" | sed "s|_|/|g" ) + echo "" >> $GITHUB_STEP_SUMMARY + echo " * ${URL_BASE}/${TRIAL_NAME_URL}/${URL_A}" >> $GITHUB_STEP_SUMMARY + echo " * ${URL_BASE}/${TRIAL_NAME_URL}/${URL_B}" >> $GITHUB_STEP_SUMMARY + echo " * etc" >> $GITHUB_STEP_SUMMARY + else + echo "### Canonical URLs will be updated by this run" >> $GITHUB_STEP_SUMMARY + URL_BASE="https://nextstrain.org" + echo "" >> $GITHUB_STEP_SUMMARY + echo " * ${URL_BASE}/${URL_A}" >> $GITHUB_STEP_SUMMARY + echo " * ${URL_BASE}/${URL_B}" >> $GITHUB_STEP_SUMMARY + echo " * etc" >> $GITHUB_STEP_SUMMARY + fi; + echo "" >> $GITHUB_STEP_SUMMARY + NOTE="NOTE: These URL paths may be incorrect if you've changed the " + NOTE+="snakemake targets in 'config/gisaid.yaml' as part of this PR. " + NOTE+="Please update this GitHub Action if so!" + echo "> $NOTE" >> $GITHUB_STEP_SUMMARY + echo "" >> $GITHUB_STEP_SUMMARY + echo "### Build (meta-)environment" >> $GITHUB_STEP_SUMMARY + if [[ "$NEXTSTRAIN_DOCKER_IMAGE" ]]; then + echo " * Docker image: $NEXTSTRAIN_DOCKER_IMAGE" >> $GITHUB_STEP_SUMMARY + else + echo " * Docker image: default (latest)" >> $GITHUB_STEP_SUMMARY + fi; + echo " * Git Branch: `${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