Phylogenetic NCBI #9
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| name: Phylogenetic NCBI | |
| defaults: | |
| run: | |
| # This is the same as GitHub Action's `bash` keyword as of 20 June 2023: | |
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsshell | |
| # | |
| # Completely spelling it out here so that GitHub can't change it out from under us | |
| # and we don't have to refer to the docs to know the expected behavior. | |
| shell: bash --noprofile --norc -eo pipefail {0} | |
| on: | |
| workflow_call: | |
| inputs: | |
| image: | |
| description: 'Specific container image to use for phylogenetic workflow (will override the default of "nextstrain build")' | |
| required: false | |
| type: string | |
| workflow_dispatch: | |
| inputs: | |
| image: | |
| description: 'Specific container image to use for ingest workflow (will override the default of "nextstrain build")' | |
| required: false | |
| type: string | |
| trial-name: | |
| description: | | |
| Trial name for deploying builds. | |
| If not set, builds will overwrite existing builds at s3://nextstrain-data/avian-flu* | |
| If set, builds will be deployed to s3://nextstrain-staging/avian-flu_trials_<trial_name>_* | |
| required: false | |
| 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/ncbi-cattle-outbreak.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: ${{ github.head_ref || github.ref_name }} | |
| phylogenetic: | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| runtime: aws-batch | |
| run: | | |
| declare -a config; | |
| if [[ "$TRIAL_NAME" ]]; then | |
| config+=( | |
| deploy_url="s3://nextstrain-staging/avian-flu_trials_${TRIAL_NAME}_" | |
| ) | |
| fi; | |
| nextstrain build \ | |
| --detach \ | |
| --no-download \ | |
| --cpus 16 \ | |
| --memory 28800mib \ | |
| . \ | |
| deploy_all \ | |
| --configfile config/h5n1-cattle-outbreak.yaml \ | |
| --config "${config[@]}" | |
| env: | | |
| NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }} | |
| TRIAL_NAME: ${{ inputs.trial-name }} | |
| artifact-name: phylogenetic-full-genome-build-output |