nf-core · mirpedrol · Dec 8, 2022 · Nov 25, 2022 · Nov 25, 2022 · Nov 25, 2022
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -0,0 +1,28 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "postCreateCommand": "python -m pip install --upgrade -r ../requirements-dev.txt -e ../ && pre-commit install --install-hooks",
+    "remoteUser": "gitpod",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/conda/bin/python",
+                "python.linting.enabled": true,
+                "python.linting.pylintEnabled": true,
+                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
+                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
+                "python.linting.flake8Path": "/opt/conda/bin/flake8",
+                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
+                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
+                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+            },
+
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
+}
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -127,3 +127,19 @@ You can replicate this process locally with the following commands:
 nf-core create -n testpipeline -d "This pipeline is for testing"
 nf-core lint nf-core-testpipeline
 ```
+
+## GitHub Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/nf-core/tools/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -33,7 +33,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 21.10.3)_
+        * Nextflow version _(eg. 22.10.1)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -1,5 +1,11 @@
 name: Create a pipeline and run nf-core linting
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
 
 # Cancel if a newer run is started
 concurrency:
@@ -17,16 +23,16 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "21.10.3"
+          - "22.10.1"
           - "latest-everything"
     steps:
       # Get the repo code
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         name: Check out source-code repository
 
       # Set up nf-core/tools
       - name: Set up Python 3.8
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
 
@@ -42,7 +48,7 @@ jobs:
           version: ${{ matrix.NXF_VER }}
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -80,7 +86,7 @@ jobs:
 
       # Run nf-core linting
       - name: nf-core lint
-        run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored --fail-warned
+        run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned
 
       # Run the other nf-core commands
       - name: nf-core list
@@ -96,13 +102,13 @@ jobs:
         run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
 
       - name: nf-core lint in release mode
-        run: nf-core --log-file log.txt lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
+        run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
 
       - name: nf-core modules install
         run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
 
       - name: nf-core modules install gitlab
-        run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch main-restructure install fastqc --force --dir nf-core-testpipeline/
+        run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch main install fastqc --force --dir nf-core-testpipeline/
 
       - name: nf-core modules list local
         run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
@@ -115,7 +121,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: nf-core-log-file
           path: log.txt
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -1,5 +1,11 @@
 name: Create a pipeline and test it
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
 
 # Cancel if a newer run is started
 concurrency:
@@ -17,14 +23,14 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "21.10.3"
+          - "22.10.1"
           - "latest-everything"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         name: Check out source-code repository
 
       - name: Set up Python 3.7
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: 3.7
 
@@ -45,7 +51,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: nf-core-log-file
           path: log.txt
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
@@ -13,11 +13,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         name: Check out source-code repository
 
       - name: Set up Python 3.7
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: 3.7
 

diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -39,11 +39,11 @@ jobs:
           options: "--color"
 
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: python-isort
-        uses: isort/isort-action@v0.1.0
+        uses: isort/isort-action@v1.0.0
         with:
           isortVersion: "latest"
           requirementsFiles: "requirements.txt requirements-dev.txt"

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
@@ -1,5 +1,11 @@
 name: Lint tools code formatting
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
 
 # Cancel if a newer run is started
 concurrency:
@@ -10,9 +16,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -24,9 +30,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -37,7 +43,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -68,14 +74,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: python-isort
-        uses: isort/isort-action@v0.1.0
+        uses: isort/isort-action@v1.1.0
         with:
           isortVersion: "latest"
           requirementsFiles: "requirements.txt requirements-dev.txt"
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev

diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest
@@ -38,5 +38,5 @@ jobs:
           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:${{ github.event.release.tag_name }}
+          docker tag nfcore/gitpod:latest nfcore/gitpod:${{ github.event.release.tag_name }}
           docker push nfcore/gitpod:${{ github.event.release.tag_name }}
diff --git a/.github/workflows/pytest-frozen-ubuntu-20.04.yml b/.github/workflows/pytest-frozen-ubuntu-20.04.yml
@@ -0,0 +1,52 @@
+name: Python tests Ubuntu-20.04 (frozen)
+# This workflow is triggered on pushes and PRs to the repository.
+# Only run if we changed a Python file
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pytest:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v3
+        name: Check out source-code repository
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.8"
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
+
+      - name: Downgrade git to the Ubuntu official repository's version
+        run: |
+          sudo apt remove git git-man
+          sudo add-apt-repository --remove ppa:git-core/ppa
+          sudo apt install git
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "latest-everything"
+
+      - name: Test with pytest
+        run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core
+
+      - uses: codecov/codecov-action@v1
+        name: Upload code coverage report
+        with:
+          if: success()
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -3,7 +3,11 @@ name: Python tests
 # Only run if we changed a Python file
 on:
   push:
+    branches:
+      - dev
   pull_request:
+  release:
+    types: [published]
 
 # Cancel if a newer run is started
 concurrency:
@@ -15,14 +19,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         name: Check out source-code repository
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 

diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml
@@ -8,7 +8,7 @@ jobs:
       - name: Check out the repo
         uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: 3.x
           cache: pip