Merge pull request #1483 from nf-core/dev

Dev > Master for v2.3.1

.editorconfig

@@ -0,0 +1,12 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,html,css,scss,js}]
+indent_size = 2

.github/CONTRIBUTING.md

@@ -11,7 +11,7 @@ If you'd like to write some code for nf-core/tools, the standard workflow
 is as follows:
 
 1. Check that there isn't [already an issue](https://github.com/nf-core/tools/issues) about your idea to avoid duplicating work.
-    * If there isn't one already, please create one so that others know you're working on this
+   - If there isn't one already, please create one so that others know you're working on this
 2. Fork the [nf-core/tools repository](https://github.com/nf-core/tools) to your GitHub account
 3. Make the necessary changes / additions within your forked repository
 4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged.
@@ -75,7 +75,7 @@ New features should also come with new tests, to keep the test-coverage high (we
 You can try running the tests locally before pushing code using the following command:
 
 ```bash
-pytest --color=yes tests/
+pytest --color=yes
 ```
 
 ### Lint Tests

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,7 +2,6 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-
   - type: markdown
     attributes:
       value: |

.github/PULL_REQUEST_TEMPLATE.md

@@ -11,7 +11,7 @@ Learn more about contributing: https://github.com/nf-core/tools/tree/master/.git
 
 ## PR checklist
 
- - [ ] This comment contains a description of changes (with reason)
- - [ ] `CHANGELOG.md` is updated
- - [ ] If you've fixed a bug or added code that should be tested, add tests!
- - [ ] Documentation in `docs` is updated
+- [ ] This comment contains a description of changes (with reason)
+- [ ] `CHANGELOG.md` is updated
+- [ ] If you've fixed a bug or added code that should be tested, add tests!
+- [ ] Documentation in `docs` is updated

.github/RELEASE_CHECKLIST.md

@@ -1,19 +1,21 @@
 ## Before release
 
 1. Check issue milestones to see outstanding issues to resolve if possible or transfer to the milestones for the next release e.g. [`v1.9`](https://github.com/nf-core/tools/issues?q=is%3Aopen+is%3Aissue+milestone%3A1.9)
-2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where *Prefix* = *Metal* and *Dictionary* = *Animal*.
+2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_.
 3. Check whether the GitHub Actions workflow scripts need updating of the Nextflow versions
-4. Create a PR to `dev` to bump the version in  `CHANGELOG.md` and `setup.py`.
+4. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py`.
 5. Make sure all CI tests are passing!
 6. Create a PR from `dev` to `master`
 7. Make sure all CI tests are passing again (additional tests are run on PRs to `master`)
 8. Request review (2 approvals required)
 9. Merge the PR into `master`
-10. Once CI tests on commit have passed, create a new release copying the `CHANGELOG` for that release into the description section.
+10. Wait for CI tests on the commit to passed
+11. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
+12. Create a new release copying the `CHANGELOG` for that release into the description section.
 
 ## After release
 
 1. Check the automated template synchronisation has been triggered properly. This should automatically open PRs directly to individual pipeline repos with the appropriate changes to update the pipeline template.
 2. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
 3. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065)
-4. Create a tools PR to `dev` to bump back to the next development version in  `CHANGELOG.md` and `setup.py`
+4. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py`

.github/workflows/create-lint-wf.yml

@@ -1,4 +1,4 @@
-name: Create a pipeline and lint it
+name: Create a pipeline and run nf-core linting
 on: [push, pull_request]
 
 env:
@@ -15,15 +15,17 @@ jobs:
         # Nextflow versions
         include:
           # Test pipeline minimum Nextflow version
-          - NXF_VER: '21.10.3'
-            NXF_EDGE: ''
+          - NXF_VER: "21.10.3"
+            NXF_EDGE: ""
           # Test latest edge release of Nextflow
-          - NXF_VER: ''
-            NXF_EDGE: '1'
+          - NXF_VER: ""
+            NXF_EDGE: "1"
     steps:
+      # Get the repo code
       - uses: actions/checkout@v2
         name: Check out source-code repository
 
+      # Set up nf-core/tools
       - name: Set up Python 3.8
         uses: actions/setup-python@v1
         with:
@@ -34,6 +36,7 @@ jobs:
           python -m pip install --upgrade pip
           pip install .
 
+      # Set up Nextflow
       - name: Install Nextflow
         env:
           NXF_VER: ${{ matrix.NXF_VER }}
@@ -44,21 +47,50 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
+      # Install the Prettier linting tools
+      - uses: actions/setup-node@v2
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      # Install the editorconfig linting tools
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      # Build a pipeline from the template
       - name: nf-core create
         run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
 
+      # Try syncing it before we change anything
+      - name: nf-core sync
+        run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/
+
+      # Build a module from the template
+      - name: nf-core modules create
+        run: nf-core --log-file log.txt modules create bpipe --dir nf-core-testpipeline --author @nf-core-bot --label process_low --meta
+
+      # Run code style linting
+      - name: Run Prettier --check
+        run: prettier --check nf-core-testpipeline
+
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(find nf-core-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+
+      # Update modules to the latest version
+      - name: nf-core modules update
+        run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview
+
+      # Run nf-core linting
       - name: nf-core lint
         run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored
 
+      # Run the other nf-core commands
       - name: nf-core list
         run: nf-core --log-file log.txt list
 
       # - name: nf-core licences
       #   run: nf-core --log-file log.txt licences nf-core-testpipeline
 
-      - name: nf-core sync
-        run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/
-
       - name: nf-core schema
         run: nf-core --log-file log.txt schema build --dir nf-core-testpipeline/ --no-prompts
 

.github/workflows/create-test-wf.yml

@@ -15,11 +15,11 @@ jobs:
         # Nextflow versions
         include:
           # Test pipeline minimum Nextflow version
-          - NXF_VER: '21.10.3'
-            NXF_EDGE: ''
+          - NXF_VER: "21.10.3"
+            NXF_EDGE: ""
           # Test latest edge release of Nextflow
-          - NXF_VER: ''
-            NXF_EDGE: '1'
+          - NXF_VER: ""
+            NXF_EDGE: "1"
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository

.github/workflows/python-lint.yml → .github/workflows/lint-code.yml

@@ -1,14 +1,35 @@
-name: Lint Python
-on:
-  push:
-    paths:
-      - '**.py'
-  pull_request:
-    paths:
-      - '**.py'
+name: Lint tools code formatting
+on: [push, pull_request]
 
 jobs:
-  PythonLint:
+  EditorConfig:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-node@v2
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      # Run editor config check only on files not covered by a linter
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
+
+  Prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-node@v2
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check ${GITHUB_WORKSPACE}
+
+  PythonBlack:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2

.github/workflows/push_dockerhub_dev.yml

@@ -20,10 +20,14 @@ jobs:
       - name: Check out code
         uses: actions/checkout@v2
 
-      - name: Build new docker image
+      - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev
 
-      - name: Push Docker image to DockerHub (dev)
+      - name: Build nfcore/gitpod:dev docker image
+        run: docker build --no-cache . --file nf_core/gitpod/gitpod.Dockerfile -t nfcore/gitpod:dev
+
+      - name: Push Docker images to DockerHub (dev)
         run: |
           echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
           docker push nfcore/tools:dev
+          docker push nfcore/gitpod:dev

.github/workflows/push_dockerhub_release.yml

@@ -20,12 +20,18 @@ jobs:
       - name: Check out code
         uses: actions/checkout@v2
 
-      - name: Build new docker image
+      - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest
 
-      - name: Push Docker image to DockerHub (release)
+      - name: Build nfcore/gitpod:latest docker image
+        run: docker build --no-cache . --file nf_core/gitpod/gitpod.Dockerfile -t nfcore/gitpod:latest
+
+      - name: Push Docker images to DockerHub (release)
         run: |
           echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
           docker push nfcore/tools:latest
           docker tag nfcore/tools:latest nfcore/tools:${{ github.event.release.tag_name }}
           docker push nfcore/tools:${{ github.event.release.tag_name }}
+          docker push nfcore/gitpod:latest
+          docker tag nfcore/gitpod:latest nfcore/tools:${{ github.event.release.tag_name }}
+          docker push nfcore/gitpod:${{ github.event.release.tag_name }}

.github/workflows/pytest.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
 
     steps:
       - uses: actions/checkout@v2

.github/workflows/tools-api-docs-dev.yml

@@ -1,7 +1,6 @@
 name: nf-core/tools dev API docs
-on:
-  push:
-    branches: [dev]
+# Run on push and PR to test that docs build
+on: [pull_request, push]
 
 jobs:
   api-docs:
@@ -27,13 +26,14 @@ jobs:
         run: make --directory ./docs/api html
 
       - name: Sync dev docs
-        if: github.repository == 'nf-core/tools'
+        # Only sync with the website if it was a push from nf-core/tools dev branch
+        if: github.repository == 'nf-core/tools' && github.event_name == 'push' && github.event.ref == 'refs/heads/dev'
         uses: SamKirkland/[email protected]
         with:
           server: ${{ secrets.ftp_server }}
           username: ${{ secrets.ftp_username}}
           password: ${{ secrets.ftp_password }}
-          local-dir: './docs/api/_build/html/'
+          local-dir: "./docs/api/_build/html/"
           server-dir: ${{ secrets.ftp_server_dir }}/dev/
           protocol: ${{ secrets.ftp_protocol }}
           port: ${{ secrets.ftp_port }}

.github/workflows/tools-api-docs-release.yml

@@ -37,7 +37,7 @@ jobs:
           server: ${{ secrets.ftp_server }}
           username: ${{ secrets.ftp_username}}
           password: ${{ secrets.ftp_password }}
-          local-dir: './docs/api/_build/html/'
+          local-dir: "./docs/api/_build/html/"
           server-dir: ${{ secrets.ftp_server_dir }}/${{ matrix.dir }}/
           protocol: ${{ secrets.ftp_protocol }}
           port: ${{ secrets.ftp_port }}