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Merge pull request #54 from nf-core/dev
PR for first release
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,108 @@ | ||
| name: nf-core CI | ||
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
| name: nf-core CI | ||
| on: | ||
| push: | ||
| branches: | ||
| - dev | ||
| - "dev" | ||
| pull_request: | ||
| branches: | ||
| - "dev" | ||
| - "master" | ||
| release: | ||
| types: [published] | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
| NFTEST_VER: "0.8.2" | ||
|
|
||
| concurrency: | ||
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | ||
| cancel-in-progress: true | ||
|
|
||
| jobs: | ||
| list: | ||
| name: List Tests | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/molkart') }}" | ||
| outputs: | ||
| # Expose matched filters as job 'modules' output variable | ||
| tests: ${{ steps.list.outputs.tests }} | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - name: Setup Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
|
|
||
| - name: Install nf-test | ||
| if: steps.cache-software.outputs.cache-hit != 'true' | ||
| run: | | ||
| wget -qO- https://code.askimed.com/install/nf-test | bash | ||
| sudo mv nf-test /usr/local/bin/ | ||
| - name: List nf-test | ||
| id: list | ||
| run: | | ||
| echo "tests=$(nf-test list --silent --format=json)" >> "$GITHUB_OUTPUT" | ||
| test: | ||
| name: Run pipeline with test data | ||
| name: ${{ matrix.tags }} (${{ matrix.profile }}-${{ matrix.NXF_VER }}) | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/molkart') }}" | ||
| if: needs.list.outputs.tests != '[]' | ||
| needs: [list] | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| NXF_VER: | ||
| - "22.10.1" | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| profile: ["docker"] #TODO add "singularity" | ||
| test: ["${{ fromJson(needs.list.outputs.tests) }}"] | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v3 | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Cache Nextflow installation | ||
| id: cache-software | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: | | ||
| /usr/local/bin/nf-test | ||
| /home/runner/.nf-test/nf-test.jar | ||
| key: molkart-${{ runner.os }}-${{ matrix.NXF_VER }} | ||
|
|
||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Run pipeline with test data | ||
| # TODO nf-core: You can customise CI pipeline run tests as required | ||
| # For example: adding multiple test runs with different parameters | ||
| # Remember that you can parallelise this by using strategy.matrix | ||
| - name: Install nf-test | ||
| if: steps.cache-software.outputs.cache-hit != 'true' | ||
| run: | | ||
| wget -qO- https://code.askimed.com/install/nf-test | bash | ||
| sudo mv nf-test /usr/local/bin/ | ||
| - name: Set up Singularity | ||
| if: matrix.profile == 'singularity' | ||
| uses: eWaterCycle/setup-singularity@v5 | ||
| with: | ||
| singularity-version: 3.7.1 | ||
|
|
||
| - name: Run nf-test | ||
| run: | | ||
| nf-test test \ | ||
| --profile="test,${{ matrix.profile }}" \ | ||
| ${{ matrix.test }} \ | ||
| --junitxml=${{ matrix.test }}-${{ matrix.profile }}.xml | ||
| - name: Publish Test Report | ||
| uses: mikepenz/action-junit-report@v3 | ||
| if: success() || failure() # run this step even if previous step failed | ||
| with: | ||
| path: ${{ matrix.test }}-${{ matrix.profile }}.xml | ||
|
|
||
| - name: Output log on failure | ||
| if: failure() | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | ||
| sudo apt install bat > /dev/null | ||
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| name: release-announcements | ||
| # Automatic release toot and tweet anouncements | ||
| on: | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
|
|
||
| jobs: | ||
| toot: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: rzr/fediverse-action@master | ||
| with: | ||
| access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} | ||
| host: "mstdn.science" # custom host if not "mastodon.social" (default) | ||
| # GitHub event payload | ||
| # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release | ||
| message: | | ||
| Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! | ||
| Please see the changelog: ${{ github.event.release.html_url }} | ||
| send-tweet: | ||
| runs-on: ubuntu-latest | ||
|
|
||
| steps: | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.10" | ||
| - name: Install dependencies | ||
| run: pip install tweepy==4.14.0 | ||
| - name: Send tweet | ||
| shell: python | ||
| run: | | ||
| import os | ||
| import tweepy | ||
| client = tweepy.Client( | ||
| access_token=os.getenv("TWITTER_ACCESS_TOKEN"), | ||
| access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), | ||
| consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), | ||
| consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), | ||
| ) | ||
| tweet = os.getenv("TWEET") | ||
| client.create_tweet(text=tweet) | ||
| env: | ||
| TWEET: | | ||
| Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! | ||
| Please see the changelog: ${{ github.event.release.html_url }} | ||
| TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} | ||
| TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} | ||
| TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} | ||
| TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} | ||
|
|
||
| bsky-post: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: zentered/[email protected] | ||
| with: | ||
| post: | | ||
| Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! | ||
| Please see the changelog: ${{ github.event.release.html_url }} | ||
| env: | ||
| BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} | ||
| BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} | ||
| # |
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