Merge pull request nf-core#3105 from mirpedrol/template-customisation…

…-codespaces

Template: add option to exclude codespaces from pipeline template

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

@@ -44,6 +44,7 @@ jobs:
           - "template_skip_code_linters.yml"
           - "template_skip_citations.yml"
           - "template_skip_gitpod.yml"
+          - "template_skip_codespaces.yml"
           - "template_skip_multiqc.yml"
           - "template_skip_changelog.yml"
         runner:
@@ -127,6 +128,10 @@ jobs:
         run: |
           printf "org: my-prefix\nskip: changelog" > create-test-lint-wf/template_skip_changelog.yml
 
+      - name: Create template skip codespaces
+        run: |
+          printf "org: my-prefix\nskip: codespaces" > create-test-lint-wf/template_skip_codespaces.yml
+
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |

CHANGELOG.md

@@ -12,6 +12,7 @@
 - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084))
 - 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 codespaces from pipeline template ([#3105](https://github.com/nf-core/tools/pull/3105))
 - 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))
 

nf_core/pipeline-template/.github/CONTRIBUTING.md

@@ -118,6 +118,7 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+{%- if codespaces %}
 
 ## GitHub Codespaces
 
@@ -133,3 +134,4 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
+  {% endif %}

nf_core/pipelines/create/create.py

@@ -103,6 +103,7 @@ def __init__(
             ],
             "citations": ["assets/methods_description_template.yml"],
             "gitpod": [".gitpod.yml"],
+            "codespaces": [".devcontainer/devcontainer.json"],
             "multiqc": [
                 "assets/multiqc_config.yml",
                 "assets/methods_description_template.yml",
@@ -220,6 +221,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
             "code_linters": {"file": True, "content": True},
             "citations": {"file": True, "content": True},
             "gitpod": {"file": True, "content": True},
+            "codespaces": {"file": True, "content": True},
             "multiqc": {"file": True, "content": True},
             "changelog": {"file": True, "content": False},
         }
@@ -520,6 +522,10 @@ def fix_linting(self):
         if not self.jinja_params["github_badges"] or not self.jinja_params["github"]:
             lint_config["readme"] = ["nextflow_badge"]
 
+        # Add codespaces specific configurations
+        if not self.jinja_params["codespaces"]:
+            lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md"])
+
         # Add multiqc specific configurations
         if not self.jinja_params["multiqc"]:
             lint_config.setdefault("files_unchanged", []).extend(

nf_core/pipelines/create/custompipeline.py

@@ -65,6 +65,13 @@
 This is useful to have all the tools ready for pipeline development.
 """
 
+markdown_codespaces = """
+The pipeline will include a devcontainer configuration.
+The devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed.
+
+Github Codespaces (https://github.com/features/codespaces) is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+"""
+
 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/
@@ -127,6 +134,12 @@ def compose(self) -> ComposeResult:
                 "Include the configuration required to use Gitpod.",
                 "gitpod",
             ),
+            PipelineFeature(
+                markdown_codespaces,
+                "Include GitHub Codespaces",
+                "The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed.",
+                "codespaces",
+            ),
             PipelineFeature(
                 markdown_multiqc,
                 "Use multiqc",

tests/data/pipeline_create_template_skip.yml

@@ -14,5 +14,6 @@ skip_features:
   - code_linters
   - citations
   - gitpod
+  - codespaces
   - multiqc
   - changelog