Merge pull request #3100 from mirpedrol/template-customisation-gitpod

Template: add option to exclude gitpod for custom pipeline template

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

@@ -42,6 +42,7 @@ jobs:
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
           - "template_skip_code_linters.yml"
+          - "template_skip_gitpod.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' }}
@@ -107,6 +108,10 @@ jobs:
         run: |
           printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml
 
+      - name: Create template skip gitpod
+        run: |
+          printf "org: my-prefix\nskip: gitpod" > create-test-lint-wf/template_skip_gitpod.yml
+
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |

CHANGELOG.md

@@ -10,6 +10,7 @@
 - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
 - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072))
 - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084))
+- add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100))
 
 ### Linting
 

nf_core/pipeline-template/nextflow.config

@@ -178,11 +178,13 @@ profiles {
         wave.freeze             = true
         wave.strategy           = 'conda,container'
     }
+    {%- if gitpod %}
     gitpod {
         executor.name           = 'local'
         executor.cpus           = 4
         executor.memory         = 8.GB
     }
+    {%- endif %}
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
 }

nf_core/pipelines/create/create.py

@@ -101,6 +101,7 @@ def __init__(
                 ".prettierrc.yml",
                 ".github/workflows/fix-linting.yml",
             ],
+            "gitpod": [".gitpod.yml"],
         }
         # 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])
@@ -210,6 +211,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
             "igenomes": {"file": True, "content": True},
             "nf_core_configs": {"file": False, "content": True},
             "code_linters": {"file": True, "content": True},
+            "gitpod": {"file": True, "content": True},
         }
 
         # Set the parameters for the jinja template

nf_core/pipelines/create/custompipeline.py

@@ -51,6 +51,13 @@
 - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).
 """
 
+markdown_gitpod = """
+Gitpod (https://www.gitpod.io/) provides standardized and automated development environments.
+
+Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements.
+This is useful to have all the tools ready for pipeline development.
+"""
+
 
 class CustomPipeline(Screen):
     """Select if the pipeline will use genomic data."""
@@ -96,6 +103,12 @@ def compose(self) -> ComposeResult:
                 "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.",
                 "code_linters",
             ),
+            PipelineFeature(
+                markdown_gitpod,
+                "Include a gitpod environment",
+                "Include the configuration required to use Gitpod.",
+                "gitpod",
+            ),
             classes="features-container",
         )
         yield Center(

tests/data/pipeline_create_template_skip.yml

@@ -12,3 +12,4 @@ skip_features:
   - igenomes
   - nf_core_configs
   - code_linters
+  - gitpod