run-pipelines #103
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name: seqera-showcase-autotest-production | |
run-name: run-pipelines | |
# Triggers workflow runs on demand, with schedule, or on push. | |
# workflow_dispatch: Manually trigger workflow from Actions tab. | |
# dryrun: Whether to do a dry run without submitting pipeline. | |
# timer: Delay before starting run. | |
# slack: Notify Slack on run completion. | |
# remove/force: Cleanup run after completion. | |
# schedule: Cron schedule to trigger runs automatically. | |
on: | |
workflow_dispatch: | |
inputs: | |
dryrun: | |
description: "Dryrun (do not submit pipeline)" | |
default: false | |
type: boolean | |
required: false | |
timer: | |
description: "Environment" | |
default: delay60mins | |
type: choice | |
options: | |
- noDelay | |
- delay1mins | |
- delay5mins | |
- delay15mins | |
- delay30mins | |
- delay60mins | |
- delay120mins | |
- delay360mins | |
- delay720mins | |
- waitForReviewer | |
slack: | |
description: Slack hook | |
type: boolean | |
required: false | |
default: true | |
remove: | |
description: Delete run | |
default: true | |
type: boolean | |
required: false | |
force: | |
description: Force delete run | |
default: false | |
type: boolean | |
required: false | |
pre_run: | |
description: Pre-run command | |
default: "" | |
type: string | |
required: false | |
config: | |
description: Nextflow config to add | |
default: "" | |
type: string | |
required: false | |
launch_container: | |
description: The container to be used to run Nextflow head job | |
default: "" | |
type: string | |
required: false | |
schedule: | |
# Every 2am | |
- cron: "0 2 * * *" | |
env: | |
TOWER_API_ENDPOINT: "https://api.cloud.seqera.io" | |
# This workflow launches pipelines in Tower, waits for completion, | |
# extracts metadata, and optionally sends Slack notifications. | |
# The 'launch' job runs the launch_pipelines.py script to start the | |
# pipelines. It uploads the Tower launch data as an artifact. | |
# The 'clearup-and-delete' job downloads the artifact, runs | |
# extract_metadata.py to collect metadata, sends Slack notifications | |
# if configured, and deletes the workflow run if configured. | |
jobs: | |
launch: | |
runs-on: ubuntu-latest | |
env: | |
TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
PRE_RUN: ${{ github.event_name != 'workflow_dispatch' && 'true' || inputs.pre_run }} | |
steps: | |
- uses: actions/checkout@v4 | |
- name: setup python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.12" | |
cache: "pip" | |
- name: install dependencies | |
run: | | |
pip install -r requirements.txt | |
- name: install tw cli | |
run: | | |
set -euo pipefail | |
wget -L https://github.com/seqeralabs/tower-cli/releases/download/v0.10.1/tw-linux-x86_64 | |
mv tw-* tw | |
chmod +x tw | |
sudo mv tw /usr/local/bin/ | |
- name: tower check | |
run: | | |
tw --version | |
- name: launch_pipelines | |
run: | | |
python launch_pipelines.py \ | |
-l DEBUG \ | |
-i \ | |
pipelines/production*.yaml \ | |
compute-envs/production*.yaml \ | |
include/*.yaml \ | |
exclude/* \ | |
${{ (github.event_name == 'workflow_dispatch' && inputs.pre_run != '') && format('--pre_run "{0}"', inputs.pre_run) || ''}} \ | |
${{ (github.event_name == 'workflow_dispatch' && inputs.config != '') && format('--config "{0}"', inputs.config) || '' }} \ | |
${{ (github.event_name == 'workflow_dispatch' && inputs.launch_container) && format('--launch-container "{0}"', inputs.launch_container) || '' }} \ | |
${{ (github.event_name == 'workflow_dispatch' && inputs.dryrun == 'true') && '--dryrun' || '' }} \ | |
-o ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}.json | |
- uses: actions/upload-artifact@v3 | |
with: | |
name: ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}_launch_json | |
path: ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}.json | |
clearup-and-delete: | |
runs-on: ubuntu-latest | |
needs: [launch] | |
environment: ${{ inputs.timer || 'delay60mins' }} | |
env: | |
TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
SLACK_BOT_TOKEN: ${{ secrets.SLACK_BOT_TOKEN }} | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/download-artifact@v3 | |
with: | |
name: ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}_launch_json | |
path: run_details | |
- name: Install tw CLI | |
run: | | |
set -euo pipefail | |
wget -L https://github.com/seqeralabs/tower-cli/releases/download/v0.9.2/tw-linux-x86_64 | |
mv tw-* tw | |
chmod +x tw | |
sudo mv tw /usr/local/bin/ | |
- name: tower check | |
run: | | |
tw --version | |
- name: setup python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.12" | |
cache: "pip" | |
- name: install dependencies | |
run: | | |
pip install -r requirements.txt | |
- name: finish workflow | |
run: | | |
python extract_metadata.py \ | |
-l DEBUG \ | |
-o ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}_workflow_data.json \ | |
-i run_details/* \ | |
--slack_channel ${{ secrets.SLACK_CHANNEL }} \ | |
${{ ( github.event_name != 'workflow_dispatch' || inputs.slack == 'true' ) && '--slack' || '' }} \ | |
${{ ( github.event_name != 'workflow_dispatch' || inputs.remove == 'true' ) && '--delete' || '' }} \ | |
${{ ( github.event_name != 'workflow_dispatch' || inputs.force == 'true' ) && '--force' || '' }} | |
- uses: actions/upload-artifact@v3 | |
with: | |
name: ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}_workflow_data | |
path: ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}_workflow_data.json |