-
Notifications
You must be signed in to change notification settings - Fork 8
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #75 from nf-core/dev
PR for release 1.3.0
- Loading branch information
Showing
82 changed files
with
9,298 additions
and
1,657 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| name: Test successful pipeline download with 'nf-core download' | ||
|
|
||
| # Run the workflow when: | ||
| # - dispatched manually | ||
| # - when a PR is opened or reopened to master branch | ||
| # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. | ||
| on: | ||
| workflow_dispatch: | ||
| inputs: | ||
| testbranch: | ||
| description: "The specific branch you wish to utilize for the test execution of nf-core download." | ||
| required: true | ||
| default: "dev" | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| - edited | ||
| - synchronize | ||
| branches: | ||
| - master | ||
| pull_request_target: | ||
| branches: | ||
| - master | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
|
|
||
| jobs: | ||
| download: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v2 | ||
|
|
||
| - name: Disk space cleanup | ||
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
|
|
||
| - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | ||
| with: | ||
| python-version: "3.12" | ||
| architecture: "x64" | ||
| - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 | ||
| with: | ||
| singularity-version: 3.8.3 | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install git+https://github.com/nf-core/tools.git@dev | ||
| - name: Get the repository name and current branch set as environment variable | ||
| run: | | ||
| echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} | ||
| echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} | ||
| echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} | ||
| - name: Download the pipeline | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| run: | | ||
| nf-core download ${{ env.REPO_LOWERCASE }} \ | ||
| --revision ${{ env.REPO_BRANCH }} \ | ||
| --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ | ||
| --compress "none" \ | ||
| --container-system 'singularity' \ | ||
| --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ | ||
| --container-cache-utilisation 'amend' \ | ||
| --download-configuration | ||
| - name: Inspect download | ||
| run: tree ./${{ env.REPOTITLE_LOWERCASE }} | ||
|
|
||
| - name: Run the downloaded pipeline (stub) | ||
| id: stub_run_pipeline | ||
| continue-on-error: true | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results | ||
| - name: Run the downloaded pipeline (stub run not supported) | ||
| id: run_pipeline | ||
| if: ${{ job.steps.stub_run_pipeline.status == failure() }} | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -4,7 +4,7 @@ on: | |
| types: [created] | ||
|
|
||
| jobs: | ||
| deploy: | ||
| fix-linting: | ||
| # Only run if comment is on a PR with the main repo, and if it contains the magic keywords | ||
| if: > | ||
| contains(github.event.comment.html_url, '/pull/') && | ||
|
|
@@ -13,43 +13,77 @@ jobs: | |
| runs-on: ubuntu-latest | ||
| steps: | ||
| # Use the @nf-core-bot token to check out so we can push later | ||
| - uses: actions/checkout@v4 | ||
| - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
| with: | ||
| token: ${{ secrets.nf_core_bot_auth_token }} | ||
|
|
||
| # indication that the linting is being fixed | ||
| - name: React on comment | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| comment-id: ${{ github.event.comment.id }} | ||
| reactions: eyes | ||
|
|
||
| # Action runs on the issue comment, so we don't get the PR by default | ||
| # Use the gh cli to check out the PR | ||
| - name: Checkout Pull Request | ||
| run: gh pr checkout ${{ github.event.issue.number }} | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | ||
|
|
||
| - uses: actions/setup-node@v4 | ||
| # Install and run pre-commit | ||
| - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Install Prettier | ||
| run: npm install -g prettier @prettier/plugin-php | ||
| - name: Install pre-commit | ||
| run: pip install pre-commit | ||
|
|
||
| # Check that we actually need to fix something | ||
| - name: Run 'prettier --check' | ||
| id: prettier_status | ||
| run: | | ||
| if prettier --check ${GITHUB_WORKSPACE}; then | ||
| echo "result=pass" >> $GITHUB_OUTPUT | ||
| else | ||
| echo "result=fail" >> $GITHUB_OUTPUT | ||
| fi | ||
| - name: Run pre-commit | ||
| id: pre-commit | ||
| run: pre-commit run --all-files | ||
| continue-on-error: true | ||
|
|
||
| - name: Run 'prettier --write' | ||
| if: steps.prettier_status.outputs.result == 'fail' | ||
| run: prettier --write ${GITHUB_WORKSPACE} | ||
| # indication that the linting has finished | ||
| - name: react if linting finished succesfully | ||
| if: steps.pre-commit.outcome == 'success' | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| comment-id: ${{ github.event.comment.id }} | ||
| reactions: "+1" | ||
|
|
||
| - name: Commit & push changes | ||
| if: steps.prettier_status.outputs.result == 'fail' | ||
| id: commit-and-push | ||
| if: steps.pre-commit.outcome == 'failure' | ||
| run: | | ||
| git config user.email "[email protected]" | ||
| git config user.name "nf-core-bot" | ||
| git config push.default upstream | ||
| git add . | ||
| git status | ||
| git commit -m "[automated] Fix linting with Prettier" | ||
| git commit -m "[automated] Fix code linting" | ||
| git push | ||
| - name: react if linting errors were fixed | ||
| id: react-if-fixed | ||
| if: steps.commit-and-push.outcome == 'success' | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| comment-id: ${{ github.event.comment.id }} | ||
| reactions: hooray | ||
|
|
||
| - name: react if linting errors were not fixed | ||
| if: steps.commit-and-push.outcome == 'failure' | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| comment-id: ${{ github.event.comment.id }} | ||
| reactions: confused | ||
|
|
||
| - name: react if linting errors were not fixed | ||
| if: steps.commit-and-push.outcome == 'failure' | ||
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
| with: | ||
| issue-number: ${{ github.event.issue.number }} | ||
| body: | | ||
| @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. | ||
| See [CI log](https://github.com/nf-core/nanostring/actions/runs/${{ github.run_id }}) for more details. | ||
Oops, something went wrong.