prettify template and printing .nf-core.yml

sanger-tol · Dec 16, 2024 · 2b2b435 · 2b2b435
1 parent 1fbd011
commit 2b2b435
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Showing 6 changed files with 9 additions and 10 deletions.
diff --git a/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml b/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:

diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
@@ -7,7 +7,7 @@
   </picture>
 </h1>
 
-{% else %}
+{%- else -%}
 
 # {{ name }}
 

diff --git a/nf_core/pipeline-template/nextflow.config b/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

diff --git a/nf_core/pipelines/bump_version.py b/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:

diff --git a/nf_core/pipelines/create/create.py b/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__)
 
@@ -380,7 +380,7 @@ 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}'")
 
     def fix_linting(self):
@@ -410,7 +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"""

diff --git a/tests/utils.py b/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