Updated linting checks

.github/workflows/linting.yml

@@ -53,9 +53,22 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: |
-          eval `ssh-agent -s`
-          ssh-add - <<< '${{ secrets.PFR_NXF_MODULES_SSH_KEY }}'
-          nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+          nf-core -l lint_log.txt lint \
+            --dir ${GITHUB_WORKSPACE} \
+            --markdown lint_results.md \
+            --key actions_ci \
+            --key actions_schema_validation \
+            --key files_exist \
+            --key files_unchanged \
+            --key merge_markers \
+            --key nextflow_config \
+            --key pipeline_name_conventions \
+            --key pipeline_todos \
+            --key readme \
+            --key schema_description \
+            --key schema_lint \
+            --key schema_params \
+            --key system_exit
 
       - name: Save PR number
         if: ${{ always() }}

.nf-core.yml

@@ -15,12 +15,10 @@ lint:
     - .github/ISSUE_TEMPLATE/bug_report.yml
     - docs/README.md
     - .github/CONTRIBUTING.md
-  multiqc_config:
-    - report_comment
+    - .github/workflows/linting.yml
   nextflow_config:
     - manifest.name
     - manifest.homePage
-  template_strings: False
 repository_type: pipeline
 template:
   prefix: plant-food-research-open