resolve merge conflicts

.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"]
+        }
+    }
+}

.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)

.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)_

.github/RELEASE_CHECKLIST.md

@@ -2,16 +2,17 @@
 
 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_.
-3. Check whether the GitHub Actions workflow scripts need updating of the Nextflow versions
+3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc)
 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. 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.
+9. Run `rich-codex` to regenerate docs screengrabs (actions `workflow_dispatch` button)
+10. Merge the PR into `master`
+11. Wait for CI tests on the commit to passed
+12. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
+13. Create a new release copying the `CHANGELOG` for that release into the description section.
 
 ## After release
 

.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 install fastqc --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

.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

.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
 
@@ -31,6 +31,6 @@ jobs:
 
       - name: Publish dist to PyPI
         if: github.repository == 'nf-core/tools'
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.pypi_password }}

.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"
@@ -55,5 +55,5 @@ jobs:
           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

.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"

.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

.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 }}

.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 }}