Merge pull request #81 from nf-core/ec-ci

Apply editorconfig and enable CI again

.github/workflows/linting.yml

@@ -17,20 +17,20 @@ jobs:
       - name: Run Markdownlint
         run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.markdownlint.yml
 
-  # EditorConfig:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v2
+  EditorConfig:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
 
-  #     - uses: actions/setup-node@v1
-  #       with:
-  #         node-version: "10"
+      - uses: actions/setup-node@v1
+        with:
+          node-version: "10"
 
-  #     - name: Install ECLint
-  #       run: npm install -g eclint
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
 
-  #     - name: Run ECLint check
-  #       run: eclint check $(git ls-files | grep -v test)
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
 
   YAML:
     runs-on: ubuntu-latest

deprecated/bedtools/intersect/main.nf

@@ -34,4 +34,3 @@ process INTERSECT_BED {
     bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
     """
 }
-

software/macs2/callpeak/main.nf

@@ -44,7 +44,7 @@ process MACS2_CALLPEAK {
         --format $format \\
         --name $prefix \\
         --treatment $ipbam \\
-         $control
+        $control
 
     macs2 --version | sed -e "s/macs2 //g" > ${software}.version.txt
     """

software/rseqc/readdistribution/main.nf

@@ -33,7 +33,7 @@ process RSEQC_READDISTRIBUTION {
     read_distribution.py \\
         -i $bam \\
         -r $bed \\
-         > ${prefix}.read_distribution.txt
+        > ${prefix}.read_distribution.txt
 
     read_distribution.py --version | sed -e "s/read_distribution.py //g" > ${software}.version.txt
     """