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Pathogen repo build #44

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Pathogen repo build

Pathogen repo build #44

Workflow file for this run

.github/workflows/pathogen-repo-build.yaml at 6a45b94
# DO NOT EDIT - GENERATED
# This workflow is intended to be called by workflows in our various pathogen
# build repos. See workflow-templates/pathogen-repo-builds.yaml (a "starter"
# workflow) in this repo for an example of what the caller workflow looks like.
name: Pathogen repo build
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:
repo:
description: >-
Repository name with owner (e.g. nextstrain/zika). Defaults to the repository of the caller workflow.
type: string
default: ${{ github.repository }}
required: false
runtime:
description: >-
Nextstrain runtime under which to run the build. Currently only supports docker, conda, and aws-batch. Defaults to "docker".
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
run:
description: >-
The full `nextstrain build` command to run for the build. Defaults to `nextstrain build .`
Use the runtime input to select the runtime for the build instead of the runtime selection options to ensure that the runtime is properly set up within the GitHub Action job.
The pathogen repo is cloned to the top level of the working directory of the GitHub Action, so use `.` to point to the pathogen repo directory.
If your build runs longer than the 6 hour limit for a single GitHub Action job, then use the aws-batch runtime and the `--detach` flag. Subsequent chained jobs will be automatically used to wait on the remote build for up to 24 hours total.
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. 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
env:
description: >-
Environment variables to set for this reusable workflow since environment variables in the caller workflow are not propagated to reusable workflows. This is expected to be a string containing YAML.
This is easily produced, for example, by pretending you're writing normal nested YAML within a literal multi-line block scalar (introduced by "|"):
with:
env: |
FOO: bar
I_CANT_BELIEVE: "it's not YAML"
would_you_believe: |
it's
not
yaml
Do not use for secrets! Instead, pass them via GitHub Action's dedicated secrets mechanism.
type: string
default: ""
required: false
artifact-name:
description: >-
Name to use for the build output artifact uploaded at end of the workflow.
If you're invoking this workflow multiple times from the same calling workflow, you should set this. Otherwise, the default "build-outputs" is probably fine.
type: string
default: build-outputs
required: false
artifact-paths:
description: >-
List of paths to include in the build output artifact uploaded at the end of the workflow, as a string following the format of the `paths` input of the `actions/upload-artifact` action. For example:
with:
artifact-paths: |
results/
auspice/
logs/
The default paths included in the artifact are:
build.log
auspice/
results/
benchmarks/
logs/
.snakemake/log/
The "build.log" contains log messages from the `nextstrain build` command. The other paths are common output paths for Nextstrain builds. If a path does not exist in your build, then the action will still succeed and will print out a warning for the non-existent file(s). Use an exclude pattern for any of the default paths that you would like to exclude from the artifact (e.g. !build.log).
This is not supported for builds on AWS Batch because the workflow detaches from the build. Please use the `nextstrain build` command locally to reattach to AWS Batch builds to download outputs.
type: string
required: false
workflow_dispatch:
inputs:
runtime:
description: >-
Nextstrain runtime under which to run the build. Currently only supports docker, conda, and aws-batch. Defaults to "docker".
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
run:
description: >-
The full `nextstrain build` command to run for the build. Defaults to `nextstrain build .`
Use the runtime input to select the runtime for the build instead of the runtime selection options to ensure that the runtime is properly set up within the GitHub Action job.
The pathogen repo is cloned to the top level of the working directory of the GitHub Action, so use `.` to point to the pathogen repo directory.
If your build runs longer than the 6 hour limit for a single GitHub Action job, then use the aws-batch runtime and the `--detach` flag. Subsequent chained jobs will be automatically used to wait on the remote build for up to 24 hours total.
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. 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
env:
description: >-
Environment variables to set for this reusable workflow since environment variables in the caller workflow are not propagated to reusable workflows. This is expected to be a string containing YAML.
This is easily produced, for example, by pretending you're writing normal nested YAML within a literal multi-line block scalar (introduced by "|"):
with:
env: |
FOO: bar
I_CANT_BELIEVE: "it's not YAML"
would_you_believe: |
it's
not
yaml
Do not use for secrets! Instead, pass them via GitHub Action's dedicated secrets mechanism.
type: string
default: ""
required: false
artifact-name:
description: >-
Name to use for the build output artifact uploaded at end of the workflow.
If you're invoking this workflow multiple times from the same calling workflow, you should set this. Otherwise, the default "build-outputs" is probably fine.
type: string
default: build-outputs
required: false
artifact-paths:
description: >-
List of paths to include in the build output artifact uploaded at the end of the workflow, as a string following the format of the `paths` input of the `actions/upload-artifact` action. For example:
with:
artifact-paths: |
results/
auspice/
logs/
The default paths included in the artifact are:
build.log
auspice/
results/
benchmarks/
logs/
.snakemake/log/
The "build.log" contains log messages from the `nextstrain build` command. The other paths are common output paths for Nextstrain builds. If a path does not exist in your build, then the action will still succeed and will print out a warning for the non-existent file(s). Use an exclude pattern for any of the default paths that you would like to exclude from the artifact (e.g. !build.log).
This is not supported for builds on AWS Batch because the workflow detaches from the build. Please use the `nextstrain build` command locally to reattach to AWS Batch builds to download outputs.
type: string
required: false
repo:
description: >-
Repository name with owner (e.g. nextstrain/zika).
type: string
default: ""
required: true
env:
NEXTSTRAIN_GITHUB_DIR: .git/nextstrain/.github
permissions:
id-token: write
jobs:
workflow-context:
runs-on: ubuntu-latest
steps:
- id: workflow-context
uses: nextstrain/.github/actions/workflow-context@master
outputs:
repository: ${{ steps.workflow-context.outputs.repository }}
sha: ${{ steps.workflow-context.outputs.sha }}
run-build:
needs: workflow-context
runs-on: ubuntu-latest
steps:
- name: Checkout build repository
uses: actions/checkout@v4
with:
repository: ${{ inputs.repo }}
- # Need to run this after the build repo is cloned so that cloning the
# build repo does not overwrite the .git dir and remove the extra support files
# that we need from nextstrain/.github repo
name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }})
uses: actions/checkout@v4
with:
repository: ${{ needs.workflow-context.outputs.repository }}
ref: ${{ needs.workflow-context.outputs.sha }}
path: ${{ env.NEXTSTRAIN_GITHUB_DIR }}
- if: inputs.env
name: Set environment variables
env:
env: ${{ inputs.env }}
run: >
# shellcheck disable=SC2154
echo "$env" | "$NEXTSTRAIN_GITHUB_DIR"/bin/yaml-to-envvars | tee -a "$GITHUB_ENV"
- name: Set secrets as environment variables
env:
secrets: ${{ toJson(secrets) }}
run: >
# shellcheck disable=SC2154
echo "$secrets" | jq 'del(.github_token)' | "$NEXTSTRAIN_GITHUB_DIR"/bin/json-to-envvars | tee -a "$GITHUB_ENV"
- if: inputs.runtime == 'aws-batch'
uses: aws-actions/configure-aws-credentials@v4
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' || '' }}
role-duration-seconds: 43200 # seconds, or 12 hours
- name: Setup runtime ${{ inputs.runtime }}
uses: ./.git/nextstrain/.github/actions/setup-nextstrain-cli
with:
cli-version: ">=7.4.0"
runtime: ${{ inputs.runtime }}
- name: Run build via ${{ inputs.runtime }}
env:
NEXTSTRAIN_BUILD_COMMAND: ${{ inputs.run }}
run: |
# shellcheck disable=SC2154
set -x
eval "$NEXTSTRAIN_BUILD_COMMAND" |& tee build.log
# Attempt to get the AWS Batch ID even if the run build command failed
# as long as the runtime is `aws-batch` and the `build.log` file exists
- if: ${{ always() && inputs.runtime == 'aws-batch' && hashFiles('build.log') != '' }}
name: Get AWS Batch job id
id: aws-batch
run: |
echo "AWS_BATCH_JOB_ID=$(sed -nE 's/.+AWS Batch Job ID\:.+ ([-a-f0-9]+)$/\1/p' < build.log)" >> "$GITHUB_ENV"
- if: ${{ always() && env.AWS_BATCH_JOB_ID }}
name: Generate AWS Batch summary
run: |
"$NEXTSTRAIN_GITHUB_DIR"/bin/interpolate-env < "$NEXTSTRAIN_GITHUB_DIR"/text-templates/attach-aws-batch.md \
> "$GITHUB_STEP_SUMMARY"
- if: always()
uses: actions/upload-artifact@v4
with:
if-no-files-found: warn
name: ${{ inputs.artifact-name }}
path: |
build.log
auspice/
results/
benchmarks/
logs/
.snakemake/log/
${{ inputs.artifact-paths }}
outputs:
AWS_BATCH_JOB_ID: ${{ env.AWS_BATCH_JOB_ID }}
# Wait for up to 6 hours (the maximum GitHub Actions job timeout¹) for the
# AWS Batch job to finish.
#
# ¹ <https://docs.github.com/en/actions/learn-github-actions/usage-limits-billing-and-administration#usage-limits>
# <https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idtimeout-minutes>
wait-1:
needs: [run-build, workflow-context]
if: needs.run-build.outputs.AWS_BATCH_JOB_ID
runs-on: ubuntu-latest
timeout-minutes: 360
steps:
# Uses needs.workflow-context.outputs
- # Need to run this after the build repo is cloned so that cloning the
# build repo does not overwrite the .git dir and remove the extra support files
# that we need from nextstrain/.github repo
name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }})
uses: actions/checkout@v4
with:
repository: ${{ needs.workflow-context.outputs.repository }}
ref: ${{ needs.workflow-context.outputs.sha }}
path: ${{ env.NEXTSTRAIN_GITHUB_DIR }}
- if: inputs.runtime == 'aws-batch'
uses: aws-actions/configure-aws-credentials@v4
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' || '' }}
role-duration-seconds: 43200 # seconds, or 12 hours
- name: Setup runtime ${{ inputs.runtime }}
uses: ./.git/nextstrain/.github/actions/setup-nextstrain-cli
with:
cli-version: ">=7.4.0"
runtime: ${{ inputs.runtime }}
- id: attach
name: Attach to AWS Batch job
env:
AWS_BATCH_JOB_ID: ${{ needs.run-build.outputs.AWS_BATCH_JOB_ID }}
run: |
# When a running process is to be cancelled (e.g. due to either user
# request or job timeout), GitHub Actions sends it SIGINT and waits
# 7.5s for it to exit.¹ We immediately detach on interrupt, letting
# the next wait-N job in our chain pick it back up (if this job timed
# out) or the cancellation job (if by user request).
#
# ¹ <https://docs.github.com/en/actions/managing-workflow-runs/canceling-a-workflow#steps-github-takes-to-cancel-a-workflow-run>
exec nextstrain build \
--aws-batch \
--attach "$AWS_BATCH_JOB_ID" \
--detach-on-interrupt \
--no-download
# Allow the workflow to be considered successful even if this job errors
# due to cancellation (timing out). Unfortunately, this doesn't
# distinguish between error from cancellation and error from command
# failure, so we work around that below.
continue-on-error: true
# Emit a "conclusion" output for the job that's based on the built-in
# conclusion (success, failure, cancelled) of the "attach" step above.
# This is the conclusion we care about for the job since the job's own
# "conclusion" is masked/transformed by "continue-on-error: true" above.
outputs:
attach-step-conclusion: ${{ steps.attach.conclusion }}
# Wait for up to another 6 hours (hours 6–12) if the preceding wait-N job
# timed out while attached to the AWS Batch job.
wait-2:
runs-on: ubuntu-latest
timeout-minutes: 360
steps:
# Uses needs.workflow-context.outputs
- # Need to run this after the build repo is cloned so that cloning the
# build repo does not overwrite the .git dir and remove the extra support files
# that we need from nextstrain/.github repo
name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }})
uses: actions/checkout@v4
with:
repository: ${{ needs.workflow-context.outputs.repository }}
ref: ${{ needs.workflow-context.outputs.sha }}
path: ${{ env.NEXTSTRAIN_GITHUB_DIR }}
- if: inputs.runtime == 'aws-batch'
uses: aws-actions/configure-aws-credentials@v4
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' || '' }}
role-duration-seconds: 43200 # seconds, or 12 hours
- name: Setup runtime ${{ inputs.runtime }}
uses: ./.git/nextstrain/.github/actions/setup-nextstrain-cli
with:
cli-version: ">=7.4.0"
runtime: ${{ inputs.runtime }}
- id: attach
name: Attach to AWS Batch job
env:
AWS_BATCH_JOB_ID: ${{ needs.run-build.outputs.AWS_BATCH_JOB_ID }}
run: |
# When a running process is to be cancelled (e.g. due to either user
# request or job timeout), GitHub Actions sends it SIGINT and waits
# 7.5s for it to exit.¹ We immediately detach on interrupt, letting
# the next wait-N job in our chain pick it back up (if this job timed
# out) or the cancellation job (if by user request).
#
# ¹ <https://docs.github.com/en/actions/managing-workflow-runs/canceling-a-workflow#steps-github-takes-to-cancel-a-workflow-run>
exec nextstrain build \
--aws-batch \
--attach "$AWS_BATCH_JOB_ID" \
--detach-on-interrupt \
--no-download
# Allow the workflow to be considered successful even if this job errors
# due to cancellation (timing out). Unfortunately, this doesn't
# distinguish between error from cancellation and error from command
# failure, so we work around that below.
continue-on-error: true
# Emit a "conclusion" output for the job that's based on the built-in
# conclusion (success, failure, cancelled) of the "attach" step above.
# This is the conclusion we care about for the job since the job's own
# "conclusion" is masked/transformed by "continue-on-error: true" above.
outputs:
attach-step-conclusion: ${{ steps.attach.conclusion }}
needs: [wait-1, run-build, workflow-context]
if: needs.wait-1.outputs.attach-step-conclusion == 'cancelled'
# 12–18 hours
wait-3:
runs-on: ubuntu-latest
timeout-minutes: 360
steps:
# Uses needs.workflow-context.outputs
- # Need to run this after the build repo is cloned so that cloning the
# build repo does not overwrite the .git dir and remove the extra support files
# that we need from nextstrain/.github repo
name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }})
uses: actions/checkout@v4
with:
repository: ${{ needs.workflow-context.outputs.repository }}
ref: ${{ needs.workflow-context.outputs.sha }}
path: ${{ env.NEXTSTRAIN_GITHUB_DIR }}
- if: inputs.runtime == 'aws-batch'
uses: aws-actions/configure-aws-credentials@v4
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' || '' }}
role-duration-seconds: 43200 # seconds, or 12 hours
- name: Setup runtime ${{ inputs.runtime }}
uses: ./.git/nextstrain/.github/actions/setup-nextstrain-cli
with:
cli-version: ">=7.4.0"
runtime: ${{ inputs.runtime }}
- id: attach
name: Attach to AWS Batch job
env:
AWS_BATCH_JOB_ID: ${{ needs.run-build.outputs.AWS_BATCH_JOB_ID }}
run: |
# When a running process is to be cancelled (e.g. due to either user
# request or job timeout), GitHub Actions sends it SIGINT and waits
# 7.5s for it to exit.¹ We immediately detach on interrupt, letting
# the next wait-N job in our chain pick it back up (if this job timed
# out) or the cancellation job (if by user request).
#
# ¹ <https://docs.github.com/en/actions/managing-workflow-runs/canceling-a-workflow#steps-github-takes-to-cancel-a-workflow-run>
exec nextstrain build \
--aws-batch \
--attach "$AWS_BATCH_JOB_ID" \
--detach-on-interrupt \
--no-download
# Allow the workflow to be considered successful even if this job errors
# due to cancellation (timing out). Unfortunately, this doesn't
# distinguish between error from cancellation and error from command
# failure, so we work around that below.
continue-on-error: true
# Emit a "conclusion" output for the job that's based on the built-in
# conclusion (success, failure, cancelled) of the "attach" step above.
# This is the conclusion we care about for the job since the job's own
# "conclusion" is masked/transformed by "continue-on-error: true" above.
outputs:
attach-step-conclusion: ${{ steps.attach.conclusion }}
needs: [wait-2, run-build, workflow-context]
if: needs.wait-2.outputs.attach-step-conclusion == 'cancelled'
# 18–24 hours
wait-4:
runs-on: ubuntu-latest
timeout-minutes: 360
steps:
# Uses needs.workflow-context.outputs
- # Need to run this after the build repo is cloned so that cloning the
# build repo does not overwrite the .git dir and remove the extra support files
# that we need from nextstrain/.github repo
name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }})
uses: actions/checkout@v4
with:
repository: ${{ needs.workflow-context.outputs.repository }}
ref: ${{ needs.workflow-context.outputs.sha }}
path: ${{ env.NEXTSTRAIN_GITHUB_DIR }}
- if: inputs.runtime == 'aws-batch'
uses: aws-actions/configure-aws-credentials@v4
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' || '' }}
role-duration-seconds: 43200 # seconds, or 12 hours
- name: Setup runtime ${{ inputs.runtime }}
uses: ./.git/nextstrain/.github/actions/setup-nextstrain-cli
with:
cli-version: ">=7.4.0"
runtime: ${{ inputs.runtime }}
- id: attach
name: Attach to AWS Batch job
env:
AWS_BATCH_JOB_ID: ${{ needs.run-build.outputs.AWS_BATCH_JOB_ID }}
run: |
# When a running process is to be cancelled (e.g. due to either user
# request or job timeout), GitHub Actions sends it SIGINT and waits
# 7.5s for it to exit.¹ We immediately detach on interrupt, letting
# the next wait-N job in our chain pick it back up (if this job timed
# out) or the cancellation job (if by user request).
#
# ¹ <https://docs.github.com/en/actions/managing-workflow-runs/canceling-a-workflow#steps-github-takes-to-cancel-a-workflow-run>
exec nextstrain build \
--aws-batch \
--attach "$AWS_BATCH_JOB_ID" \
--detach-on-interrupt \
--no-download
# Allow the workflow to be considered successful even if this job errors
# due to cancellation (timing out). Unfortunately, this doesn't
# distinguish between error from cancellation and error from command
# failure, so we work around that below.
continue-on-error: true
# Emit a "conclusion" output for the job that's based on the built-in
# conclusion (success, failure, cancelled) of the "attach" step above.
# This is the conclusion we care about for the job since the job's own
# "conclusion" is masked/transformed by "continue-on-error: true" above.
outputs:
attach-step-conclusion: ${{ steps.attach.conclusion }}
needs: [wait-3, run-build, workflow-context]
if: needs.wait-3.outputs.attach-step-conclusion == 'cancelled'
# Since the wait-N jobs use "continue-on-error: true" out of necessity (to
# avoid failing the whole workflow when they time out and get cancelled), we
# use a final job here to succeed or fail the whole workflow based on the
# aggregate of their "attach" step conclusions.
wait-conclusion:
needs: [wait-1, wait-2, wait-3, wait-4]
if: always()
runs-on: ubuntu-latest
steps:
- name: All attach steps in wait-N jobs were successful (or skipped)
run: |
# shellcheck disable=SC2242
exit ${{ contains(needs.*.outputs.attach-step-conclusion, 'failure') && '1' || '0' }}
# XXX TODO: Jobs can fall off the end of our wait-N chain and appear to be
# successful/complete in GitHub but still running on AWS. Probably very
# rare in reality, though, for an AWS job to take longer than 24h?
# -trs, 12 Sept 2023
# Cancel the AWS Batch job if the GitHub workflow run is cancelled.
#
# We depend on the last wait-N job (wait-4) so that this job doesn't get
# skipped immediately after run-build. It needs to be at the end of the
# chain.
cancellation:
needs: [wait-4, run-build, workflow-context]
if: cancelled()
runs-on: ubuntu-latest
steps:
# Uses needs.workflow-context.outputs
- # Need to run this after the build repo is cloned so that cloning the
# build repo does not overwrite the .git dir and remove the extra support files
# that we need from nextstrain/.github repo
name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }})
uses: actions/checkout@v4
with:
repository: ${{ needs.workflow-context.outputs.repository }}
ref: ${{ needs.workflow-context.outputs.sha }}
path: ${{ env.NEXTSTRAIN_GITHUB_DIR }}
- if: inputs.runtime == 'aws-batch'
uses: aws-actions/configure-aws-credentials@v4
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' || '' }}
role-duration-seconds: 43200 # seconds, or 12 hours
- name: Setup runtime ${{ inputs.runtime }}
uses: ./.git/nextstrain/.github/actions/setup-nextstrain-cli
with:
cli-version: ">=7.4.0"
runtime: ${{ inputs.runtime }}
- id: cancel
name: Cancel AWS Batch job
env:
AWS_BATCH_JOB_ID: ${{ needs.run-build.outputs.AWS_BATCH_JOB_ID }}
run: |
# `nextstrain` will stay attached while it waits for cancellation to
# occur, before finally exiting non-zero. In the unlikely event that
# the job completes before cancellation can occur, it'll exit 0, and
# we want to treat that as an error.
nextstrain build --aws-batch --attach "$AWS_BATCH_JOB_ID" --cancel \
&& exit 1 \
|| exit 0
# The cancellation job may fail, but we don't want that to impact the
# overall workflow run status.
continue-on-error: true