Fix pre commit template

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Template
 
 - Use outputs instead of the environment to pass around values between steps in the Download Test Action ([#3351](https://github.com/nf-core/tools/pull/3351))
+- Fix pre commit template ([#3358](https://github.com/nf-core/tools/pull/3358))
 
 ### Download
 

nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -11,7 +11,6 @@ body:
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
         - [{{ name }} pipeline documentation](https://nf-co.re/{{ short_name }}/usage)
 {%- endif %}
-
   - type: textarea
     id: description
     attributes:

nf_core/pipeline-template/.gitpod.yml

@@ -3,7 +3,7 @@ tasks:
   - name: Update Nextflow and setup pre-commit
     command: |
       pre-commit install --install-hooks
-      nextflow self-update {% if code_linters %}
+      nextflow self-update {%- if code_linters %}
 
 vscode:
   extensions:

nf_core/pipeline-template/.prettierignore

@@ -16,3 +16,6 @@ testing/
 testing*
 *.pyc
 bin/
+{%- if rocrate %}
+ro-crate-metadata.json
+{%- endif %}

nf_core/pipeline-template/README.md

@@ -7,7 +7,7 @@
   </picture>
 </h1>
 
-{% else %}
+{%- else -%}
 
 # {{ name }}
 

nf_core/pipeline-template/nextflow.config

@@ -306,7 +306,7 @@ validation {
         command = "nextflow run {{ name }} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
-        {% if is_nfcore -%}
+        {%- if is_nfcore %}
         beforeText = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

@@ -143,7 +143,7 @@ workflow PIPELINE_COMPLETION {
     {%- if multiqc %}
     def multiqc_reports = multiqc_report.toList()
     {%- endif %}
-    
+
     //
     // Completion email and summary
     //

nf_core/pipelines/bump_version.py

@@ -12,7 +12,7 @@
 
 import nf_core.utils
 from nf_core.pipelines.rocrate import ROCrate
-from nf_core.utils import Pipeline
+from nf_core.utils import Pipeline, custom_yaml_dumper
 
 log = logging.getLogger(__name__)
 stderr = rich.console.Console(stderr=True, force_terminal=nf_core.utils.rich_force_colors())
@@ -257,7 +257,7 @@ def update_yaml_file(fn: Path, patterns: List[Tuple[str, str]], yaml_key: List[s
         if new_value != current_value:
             target[last_key] = new_value
             with open(fn, "w") as file:
-                yaml.dump(yaml_content, file)
+                yaml.dump(yaml_content, file, Dumper=custom_yaml_dumper())
             log.info(f"Updated version in YAML file '{fn}'")
             log_change(str(current_value), str(new_value))
     except KeyError as e:

nf_core/pipelines/create/create.py

@@ -22,7 +22,7 @@
 from nf_core.pipelines.create_logo import create_logo
 from nf_core.pipelines.lint_utils import run_prettier_on_file
 from nf_core.pipelines.rocrate import ROCrate
-from nf_core.utils import NFCoreTemplateConfig, NFCoreYamlLintConfig
+from nf_core.utils import NFCoreTemplateConfig, NFCoreYamlLintConfig, custom_yaml_dumper
 
 log = logging.getLogger(__name__)
 
@@ -266,6 +266,11 @@ def init_pipeline(self):
         # Init the git repository and make the first commit
         if not self.no_git:
             self.git_init_pipeline()
+            # Run prettier on files
+            current_dir = Path.cwd()
+            os.chdir(self.outdir)
+            run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])
+            os.chdir(current_dir)
 
         if self.config.is_nfcore and not self.is_interactive:
             log.info(
@@ -375,12 +380,9 @@ def render_template(self) -> None:
             if config_fn is not None and config_yml is not None:
                 with open(str(config_fn), "w") as fh:
                     config_yml.template = NFCoreTemplateConfig(**self.config.model_dump(exclude_none=True))
-                    yaml.safe_dump(config_yml.model_dump(exclude_none=True), fh)
+                    yaml.dump(config_yml.model_dump(exclude_none=True), fh, Dumper=custom_yaml_dumper())
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
 
-        # Run prettier on files
-        run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])
-
     def fix_linting(self):
         """
         Updates the .nf-core.yml with linting configurations
@@ -408,7 +410,7 @@ def fix_linting(self):
         if config_fn is not None and nf_core_yml is not None:
             nf_core_yml.lint = NFCoreYamlLintConfig(**lint_config)
             with open(self.outdir / config_fn, "w") as fh:
-                yaml.dump(nf_core_yml.model_dump(exclude_none=True), fh, default_flow_style=False, sort_keys=False)
+                yaml.dump(nf_core_yml.model_dump(exclude_none=True), fh, Dumper=custom_yaml_dumper())
 
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""

nf_core/pipelines/lint_utils.py

@@ -97,7 +97,7 @@ def run_prettier_on_file(file: Union[Path, str, List[str]]) -> None:
             all_lines = [line for line in e.stdout.decode().split("\n")]
             files = "\n".join(all_lines[3:])
             log.debug(f"The following files were modified by prettier:\n {files}")
-        elif e.stderr.decode():
+        else:
             log.warning(
                 "There was an error running the prettier pre-commit hook.\n"
                 f"STDOUT: {e.stdout.decode()}\nSTDERR: {e.stderr.decode()}"

tests/utils.py

@@ -14,7 +14,7 @@
 import nf_core.modules
 import nf_core.pipelines.create.create
 from nf_core import __version__
-from nf_core.utils import NFCoreTemplateConfig, NFCoreYamlConfig
+from nf_core.utils import NFCoreTemplateConfig, NFCoreYamlConfig, custom_yaml_dumper
 
 TEST_DATA_DIR = Path(__file__).parent / "data"
 OLD_TRIMGALORE_SHA = "9b7a3bdefeaad5d42324aa7dd50f87bea1b04386"
@@ -136,7 +136,7 @@ def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]:
         bump_version=None,
     )
     with open(str(Path(pipeline_dir, ".nf-core.yml")), "w") as fh:
-        yaml.dump(nf_core_yml.model_dump(), fh)
+        yaml.dump(nf_core_yml.model_dump(), fh, Dumper=custom_yaml_dumper())
 
     nf_core.pipelines.create.create.PipelineCreate(
         pipeline_name, "it is mine", "me", no_git=no_git, outdir=pipeline_dir, force=True