Add editorconfig linting to tools CI tests

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

@@ -47,12 +47,16 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
-      # Install the Prettier linting stuff
+      # 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"
@@ -69,6 +73,9 @@ jobs:
       - 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

.github/workflows/lint-code.yml

@@ -2,6 +2,20 @@ name: Lint tools code formatting
 on: [push, pull_request]
 
 jobs:
+  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:

Dockerfile

@@ -1,6 +1,6 @@
-FROM python:3.8.9-slim 
+FROM python:3.8.9-slim
 LABEL authors="phil.ewels@scilifelab.se,erik.danielsson@scilifelab.se" \
-      description="Docker image containing requirements for the nfcore tools"
+    description="Docker image containing requirements for the nfcore tools"
 
 # Do not pick up python packages from $HOME
 ENV PYTHONNUSERSITE=1
@@ -14,23 +14,23 @@ RUN python -m pip install -r requirements.txt
 
 # Install Nextflow dependencies
 RUN apt-get update \
-      && apt-get upgrade -y \
-      && apt-get install -y git \
-      && apt-get install -y curl
+    && apt-get upgrade -y \
+    && apt-get install -y git \
+    && apt-get install -y curl
 
-# Create man dir required for Java installation 
+# Create man dir required for Java installation
 # and install Java
 RUN mkdir -p /usr/share/man/man1 \
-      && apt-get install -y  openjdk-11-jre \
-      && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+    && apt-get install -y  openjdk-11-jre \
+    && apt-get clean -y && rm -rf /var/lib/apt/lists/*
 
 # Setup ARG for NXF_VER ENV
 ARG NXF_VER=""
 ENV NXF_VER ${NXF_VER}
 # Install Nextflow
 RUN curl -s https://get.nextflow.io | bash \
-      && mv nextflow /usr/local/bin \
-      && chmod a+rx /usr/local/bin/nextflow
+    && mv nextflow /usr/local/bin \
+    && chmod a+rx /usr/local/bin/nextflow
 # Add the nf-core source files to the image
 COPY . /usr/src/nf_core
 WORKDIR /usr/src/nf_core

MANIFEST.in

@@ -2,4 +2,4 @@ include LICENSE
 include README.md
 graft nf_core/module-template
 graft nf_core/pipeline-template
-include requirements.txt
+include requirements.txt

nf_core/module-template/tests/main.nf

@@ -6,9 +6,9 @@ include { {{ tool_name_underscore|upper }} } from '../../../{{ "../" if subtool
 
 workflow test_{{ tool_name_underscore }} {
     {% if has_meta %}
-    input = [ 
+    input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
     ]
     {%- else %}
     input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)

nf_core/pipeline-template/.github/workflows/linting.yml

@@ -20,7 +20,7 @@ jobs:
         run: npm install -g editorconfig-checker
 
       - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
+        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
 
   Prettier:
     runs-on: ubuntu-latest

nf_core/pipeline-template/assets/email_template.html

@@ -4,6 +4,7 @@
     <meta http-equiv="X-UA-Compatible" content="IE=edge" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
 
+    <!-- prettier-ignore -->
     <meta name="description" content="{{ name }}: {{ description }}" />
     <title>{{ name }} Pipeline Report</title>
   </head>

pyproject.toml

@@ -1,17 +1,17 @@
 [build-system]
-build-backend = 'setuptools.build_meta'
+build-backend = "setuptools.build_meta"
 requires = [
-  'setuptools>=40.6.0',
-  'wheel'
+    "setuptools>=40.6.0",
+    "wheel"
 ]
 
 [tool.black]
 line-length = 120
-target_version = ['py36','py37','py38']
+target_version = ["py36","py37","py38"]
 
 [tool.pytest.ini_options]
 markers = [
     "datafiles: load datafiles"
 ]
 testpaths = ["tests"]
-norecursedirs = [ '.*', 'build', 'dist', '*.egg', 'data', '__pycache__', '.github', 'nf_core', 'docs']
+norecursedirs = [ ".*", "build", "dist", "*.egg", "data", "__pycache__", ".github", "nf_core", "docs"]

requirements-dev.txt

@@ -4,4 +4,4 @@ pytest-cov
 mock
 black
 Sphinx
-sphinx_rtd_theme
+sphinx_rtd_theme