more prettier fixes

nf_core/pipeline-template/CITATIONS.md

@@ -18,7 +18,7 @@
 
 {%- endif %}
 
-{% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+{%- if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 

nf_core/pipeline-template/docs/output.md

@@ -2,7 +2,7 @@
 
 ## Introduction
 
-This document describes the output produced by the pipeline. {% if multiqc %}Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.{% endif %}
+This document describes the output produced by the pipeline.{% if multiqc %} Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.{% endif %}
 
 The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
@@ -14,9 +14,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 {% if fastqc -%}
 
-- [FastQC](#fastqc) - Raw read QC
-  {%- endif %}
-  {%- if multiqc %}
+- [FastQC](#fastqc) - Raw read QC{% endif %}
+  {%- if multiqc -%}
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
   {%- endif %}
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
@@ -35,7 +34,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 </details>
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
-{%- endif %}
+{%- endif -%}
 
 {% if multiqc -%}
 
@@ -54,7 +53,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
 
 Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
-{%- endif %}
+{%- endif -%}
 
 ### Pipeline information
 

nf_core/pipeline-template/docs/usage.md

@@ -115,7 +115,7 @@ It is a good idea to specify the pipeline version when running the pipeline on y
 
 First, go to the [{{ name }} releases page](https://github.com/{{ name }}/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
-This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. {% if multiqc %}For example, at the bottom of the MultiQC reports.{% endif %}
+This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.{% if multiqc %} For example, at the bottom of the MultiQC reports.{% endif %}
 
 To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 

nf_core/pipelines/create/create.py

@@ -267,10 +267,8 @@ def init_pipeline(self):
         if not self.no_git:
             self.git_init_pipeline()
             # Run prettier on files
-            if (
-                self.config.skip_features is None
-                or "code_linters" not in self.config.skip_features
-                or "github" not in self.config.skip_features
+            if self.config.skip_features is None or not (
+                "code_linters" in self.config.skip_features or "github" in self.config.skip_features
             ):
                 current_dir = Path.cwd()
                 os.chdir(self.outdir)
@@ -415,7 +413,13 @@ 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, Dumper=custom_yaml_dumper())
+                yaml.dump(
+                    nf_core_yml.model_dump(exclude_none=True),
+                    fh,
+                    sort_keys=False,
+                    default_flow_style=False,
+                    Dumper=custom_yaml_dumper(),
+                )
 
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""

nf_core/pipelines/create/template_features.yml

@@ -148,6 +148,10 @@ is_nfcore:
       - "docs/images/nf-core-{{short_name}}_logo_light.png"
       - "docs/images/nf-core-{{short_name}}_logo_dark.png"
       - ".github/ISSUE_TEMPLATE/bug_report.yml"
+      - ".github/CONTRIBUTING.md"
+      - ".github/PULL_REQUEST_TEMPLATE.md"
+      - "assets/email_template.txt"
+      - "docs/README.md"
     nextflow_config:
       - "manifest.name"
       - "manifest.homePage"
@@ -445,6 +449,8 @@ rocrate:
   linting:
     files_warn:
       - "ro-crate-metadata.json"
+    files_unchanged:
+      - ".prettierignore"
 vscode:
   skippable_paths:
     - ".vscode"