Sync template #70
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name: Sync template | |
on: | |
release: | |
types: [published] | |
workflow_dispatch: | |
inputs: | |
testpipeline: | |
type: boolean | |
description: Only run on nf-core/testpipeline? | |
required: true | |
runners: | |
description: "Runners to test on" | |
type: choice | |
options: | |
- "ubuntu-latest" | |
- "self-hosted" | |
default: "self-hosted" | |
force_pr: | |
description: "Force a PR to be created" | |
type: boolean | |
default: false | |
pipeline: | |
description: "Pipeline to sync" | |
type: string | |
default: "all" | |
# Cancel if a newer run is started | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
jobs: | |
get-pipelines: | |
runs-on: "ubuntu-latest" | |
outputs: | |
matrix: ${{ steps.set-matrix.outputs.matrix }} | |
steps: | |
- id: set-matrix | |
run: | | |
if [ "${{ github.event.inputs.testpipeline }}" == "true" ]; then | |
echo '{"pipeline":["testpipeline"]}' > pipeline_names.json | |
elif [ "${{ github.event.inputs.pipeline }}" != "all" ]; then | |
curl -O https://nf-co.re/pipeline_names.json | |
# check if the pipeline exists | |
if ! grep -q "\"${{ github.event.inputs.pipeline }}\"" pipeline_names.json; then | |
echo "Pipeline ${{ github.event.inputs.pipeline }} does not exist" | |
exit 1 | |
fi | |
echo '{"pipeline":["${{ github.event.inputs.pipeline }}"]}' > pipeline_names.json | |
else | |
curl -O https://nf-co.re/pipeline_names.json | |
fi | |
echo "matrix=$(cat pipeline_names.json)" >> $GITHUB_OUTPUT | |
sync: | |
needs: get-pipelines | |
# use the github runner on release otherwise use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default | |
runs-on: ${{github.event_name == 'release' && 'self-hosted' || github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
strategy: | |
matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}} | |
fail-fast: false | |
steps: | |
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
name: Check out nf-core/tools | |
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
name: Check out nf-core/${{ matrix.pipeline }} | |
with: | |
repository: nf-core/${{ matrix.pipeline }} | |
ref: dev | |
token: ${{ secrets.nf_core_bot_auth_token }} | |
path: nf-core/${{ matrix.pipeline }} | |
fetch-depth: "0" | |
- name: Set up Python 3.12 | |
uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | |
with: | |
python-version: "3.12" | |
- name: Install python dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install . | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v2 | |
with: | |
version: "latest-everything" | |
- name: Run synchronisation | |
if: github.repository == 'nf-core/tools' | |
env: | |
GITHUB_AUTH_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | |
run: | | |
git config --global user.email "core@nf-co.re" | |
git config --global user.name "nf-core-bot" | |
nf-core --log-file sync_log_${{ matrix.pipeline }}.txt pipelines sync -d nf-core/${{ matrix.pipeline }} \ | |
--from-branch dev \ | |
--pull-request \ | |
--username nf-core-bot \ | |
--github-repository nf-core/${{ matrix.pipeline }} | |
- name: Upload sync log file artifact | |
if: ${{ always() }} | |
uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 | |
with: | |
name: sync_log_${{ matrix.pipeline }} | |
path: sync_log_${{ matrix.pipeline }}.txt |