Merge pull request nf-core#3104 from mirpedrol/template-customisation…

…-changelog

Template: add option to exclude changelog from custom pipeline template

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

@@ -45,6 +45,7 @@ jobs:
  - "template_skip_citations.yml"
  - "template_skip_gitpod.yml"
  - "template_skip_multiqc.yml"
+ - "template_skip_changelog.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' }}
@@ -122,6 +123,10 @@ jobs:
  run: |
  printf "org: my-prefix\nskip: multiqc" > create-test-lint-wf/template_skip_multiqc.yml
 
+ - name: Create template skip changelog
+ run: |
+ printf "org: my-prefix\nskip: changelog" > create-test-lint-wf/template_skip_changelog.yml
+
  # Create a pipeline from the template
  - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
  run: |

CHANGELOG.md

@@ -13,6 +13,7 @@
 - add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101))
 - add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100))
 - add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103))
+- add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104))
 
 ### Linting
 

nf_core/pipelines/create/create.py

@@ -108,6 +108,7 @@ def __init__(
  "assets/methods_description_template.yml",
  "modules/nf-core/multiqc/",
  ],
+ "changelog": ["CHANGELOG.md"],
  }
  # 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])
@@ -220,6 +221,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
  "citations": {"file": True, "content": True},
  "gitpod": {"file": True, "content": True},
  "multiqc": {"file": True, "content": True},
+ "changelog": {"file": True, "content": False},
  }
 
  # Set the parameters for the jinja template
@@ -526,6 +528,10 @@ def fix_linting(self):
  lint_config.setdefault("files_exist", []).extend(["assets/multiqc_config.yml"])
  lint_config["multiqc_config"] = False
 
+ # Add changelog specific configurations
+ if not self.jinja_params["changelog"]:
+ lint_config["files_exist"].extend(["CHANGELOG.md"])
+
  # If the pipeline is not nf-core
  if not self.config.is_nfcore:
  lint_config["files_unchanged"].extend([".github/ISSUE_TEMPLATE/bug_report.yml"])

nf_core/pipelines/create/custompipeline.py

@@ -65,6 +65,11 @@
 This is useful to have all the tools ready for pipeline development.
 """
 
+markdown_changelog = """
+Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version.
+You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/
+"""
+
 
 class CustomPipeline(Screen):
  """Select if the pipeline will use genomic data."""
@@ -128,6 +133,12 @@ def compose(self) -> ComposeResult:
  "The pipeline will include the MultiQC module which generates an HTML report for quality control.",
  "multiqc",
  ),
+ PipelineFeature(
+ markdown_changelog,
+ "Add a changelog",
+ "Add a CHANGELOG.md file.",
+ "changelog",
+ ),
  classes="features-container",
  )
  yield Center(

tests/data/pipeline_create_template_skip.yml

@@ -15,3 +15,4 @@ skip_features:
  - citations
  - gitpod
  - multiqc
+ - changelog