add option to skip code linters

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

@@ -41,6 +41,7 @@ jobs:
           - "template_skip_github_badges.yml"
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
+          - "template_skip_code_linters.yml"
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
@@ -102,6 +103,10 @@ jobs:
         run: |
           printf "org: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml
 
+      - name: Create template skip code_linters
+        run: |
+          printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml
+
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |

nf_core/pipeline-template/.gitpod.yml

@@ -10,8 +10,9 @@ tasks:
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
+    #{%- if code_linters -%}
     - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
+    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files{% endif %}
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
     # - nextflow.nextflow                    # Nextflow syntax highlighting

nf_core/pipelines/create/create.py

@@ -94,6 +94,13 @@ def __init__(
                 ".github/workflows/awstest.yml",
                 ".github/workflows/release-announcements.yml",
             ],
+            "code_linters": [
+                ".editorconfig",
+                ".pre-commit-config.yaml",
+                ".prettierignore",
+                ".prettierrc.yml",
+                ".github/workflows/fix-linting.yml",
+            ],
         }
         # Get list of files we're skipping with the supplied skip keys
         self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k])
@@ -202,6 +209,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
             "github_badges": {"file": False, "content": True},
             "igenomes": {"file": True, "content": True},
             "nf_core_configs": {"file": False, "content": True},
+            "code_linters": {"file": True, "content": True},
         }
 
         # Set the parameters for the jinja template

nf_core/pipelines/create/custompipeline.py

@@ -41,6 +41,16 @@
 For more information about nf-core configuration profiles, see the [nf-core/configs repository](https://github.com/nf-core/configs)
 """
 
+markdown_code_linters = """
+Pipelines include code linters, these linters will check the formatting of your code.
+Linters will check JSON, YAML, Python and others.
+The available code linters are:
+
+- pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository.
+- editor-config (https://github.com/editorconfig-checker/editorconfig-checker): checks rules such as indentation or trailing spaces.
+- prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).
+"""
+
 
 class CustomPipeline(Screen):
     """Select if the pipeline will use genomic data."""
@@ -80,6 +90,12 @@ def compose(self) -> ComposeResult:
                 "The pipeline will include configuration profiles containing custom parameters requried to run nf-core pipelines at different institutions",
                 "nf_core_configs",
             ),
+            PipelineFeature(
+                markdown_code_linters,
+                "Use code linters",
+                "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.",
+                "code_linters",
+            ),
             classes="features-container",
         )
         yield Center(

tests/data/pipeline_create_template_skip.yml

@@ -11,3 +11,4 @@ skip_features:
   - github_badges
   - igenomes
   - nf_core_configs
+  - code_linters

tests/test_create.py

@@ -106,14 +106,16 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path):
         pipeline.init_pipeline()
 
         # Check pipeline template yml has been dumped to `.nf-core.yml` and matches input
-        assert not os.path.exists(os.path.join(pipeline.outdir, "pipeline_template.yml"))
-        assert os.path.exists(os.path.join(pipeline.outdir, ".nf-core.yml"))
-        with open(os.path.join(pipeline.outdir, ".nf-core.yml")) as fh:
+        assert not os.path.exists(Path(pipeline.outdir / "pipeline_template.yml"))
+        assert os.path.exists(Path(pipeline.outdir / ".nf-core.yml"))
+        with open(Path(pipeline.outdir / ".nf-core.yml")) as fh:
             nfcore_yml = yaml.safe_load(fh)
             assert "template" in nfcore_yml
             assert yaml.safe_load(PIPELINE_TEMPLATE_YML.read_text()).items() <= nfcore_yml["template"].items()
 
         # Check that some of the skipped files are not present
-        assert not os.path.exists(os.path.join(pipeline.outdir, "CODE_OF_CONDUCT.md"))
-        assert not os.path.exists(os.path.join(pipeline.outdir, ".github"))
-        assert not os.path.exists(os.path.join(pipeline.outdir, "conf", "igenomes.config"))
+        assert not os.path.exists(Path(pipeline.outdir / "CODE_OF_CONDUCT.md"))
+        assert not os.path.exists(Path(pipeline.outdir / ".github"))
+        assert not os.path.exists(Path(pipeline.outdir / "conf" / "igenomes.config"))
+        assert not os.path.exists(Path(pipeline.outdir / ".editorconfig"))
+        assert not os.path.exists(Path(pipeline.outdir / ".editorconfig"))