Template: Add tests to ensure all files are part of a template customisation group and all groups are tested

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

@@ -44,7 +44,7 @@ jobs:
       - name: Create Matrix
         id: create_matrix
         run: |
-          echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
+          echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/template_features.yml)" >> $GITHUB_OUTPUT
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}

CHANGELOG.md

@@ -36,6 +36,7 @@
 - add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
 - add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133))
 - add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
+- Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
 
 ### Linting
 

MANIFEST.in

@@ -10,4 +10,4 @@ include nf_core/assets/logo/nf-core-repo-logo-base-darkbg.png
 include nf_core/assets/logo/placeholder_logo.svg
 include nf_core/assets/logo/MavenPro-Bold.ttf
 include nf_core/pipelines/create/create.tcss
-include nf_core/pipelines/create/templatefeatures.yml
+include nf_core/pipelines/create/template_features.yml

nf_core/pipeline-template/README.md

@@ -7,6 +7,10 @@
   </picture>
 </h1>
 
+{%- else %}
+
+# {{ name }}
+
 {% endif -%}
 {% if github_badges -%}
 [![GitHub Actions CI Status](https://github.com/{{ name }}/actions/workflows/ci.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/ci.yml)

nf_core/pipeline-template/nextflow.config

@@ -31,14 +31,14 @@ params {
 
     // Boilerplate options
     outdir                       = null
-    publish_dir_mode             = 'copy'
+    {% if modules %}publish_dir_mode             = 'copy'{% endif %}
     {%- if email %}
     email                        = null
     email_on_fail                = null
     plaintext_email              = false
     {%- endif %}
-    monochrome_logs              = false
-    hook_url                     = null
+    {% if modules %}monochrome_logs              = false{% endif %}
+    {% if slackreport or adaptivecard %}hook_url                     = null{% endif %}
     {% if nf_schema %}help                         = false
     help_full                    = false
     show_hidden                  = false{% endif %}
@@ -62,9 +62,10 @@ params {
     max_cpus                   = 16
     max_time                   = '240.h'
 
+    {%- if nf_schema %}
     // Schema validation default options
     validate_params            = true
-
+    {% endif %}
 }
 {% if modules %}
 // Load base.config by default for all pipelines

nf_core/pipeline-template/nextflow_schema.json

@@ -184,6 +184,7 @@
                     "fa_icon": "fas fa-question-circle",
                     "hidden": true
                 },
+                {%- if modules %}
                 "publish_dir_mode": {
                     "type": "string",
                     "default": "copy",
@@ -192,7 +193,7 @@
                     "fa_icon": "fas fa-copy",
                     "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
-                },{% if email %}
+                },{% endif %}{% if email %}
                 "email_on_fail": {
                     "type": "string",
                     "description": "Email address for completion summary, only when pipeline fails.",
@@ -215,21 +216,22 @@
                     "default": "25.MB",
                     "fa_icon": "fas fa-file-upload",
                     "hidden": true
-                },
-                {% endif %}
+                },{% endif %}
+                {%- if modules %}
                 "monochrome_logs": {
                     "type": "boolean",
                     "description": "Do not use coloured log outputs.",
                     "fa_icon": "fas fa-palette",
                     "hidden": true
-                },
+                },{% endif %}
+                {%- if slackreport or adaptivecard %}
                 "hook_url": {
                     "type": "string",
                     "description": "Incoming hook URL for messaging service",
                     "fa_icon": "fas fa-people-group",
                     "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                     "hidden": true
-                },
+                },{% endif %}
                 {%- if multiqc %}
                 "multiqc_config": {
                     "type": "string",

nf_core/pipelines/create/templatefeatures.yml → nf_core/pipelines/create/template_features.yml

@@ -1,18 +1,25 @@
 github:
   skippable_paths:
-    - ".github/"
-    - ".gitignore"
-  short_description: "Skip the creation of a local Git repository."
-  description: ""
-  help_text: ""
+    - ".github"
+    - ".gitattributes"
+  short_description: "Use a GitHub repository."
+  description: "Create a GitHub repository for the pipeline."
+  help_text: |
+    This will create a GitHub repository for the pipeline.
+
+    The repository will include:
+    - Continuous Integration (CI) tests
+    - Issues and pull requests templates
+
+    The initialisation of a git repository is required to use the nf-core/tools.
+    This means that even if you unselect this option, your pipeline will still contain a `.git` directory and `.gitignore` file.
   linting:
     files_exist:
       - ".github/ISSUE_TEMPLATE/bug_report.yml"
       - ".github/ISSUE_TEMPLATE/feature_request.yml"
       - ".github/PULL_REQUEST_TEMPLATE.md"
       - ".github/CONTRIBUTING.md"
       - ".github/.dockstore.yml"
-      - ".gitignore"
     files_unchanged:
       - ".github/ISSUE_TEMPLATE/bug_report.yml"
       - ".github/ISSUE_TEMPLATE/config.yml"
@@ -26,7 +33,7 @@ github:
     readme:
       - "nextflow_badge"
   nfcore_pipelines: False
-  custom_pipelines: False
+  custom_pipelines: True
 ci:
   skippable_paths:
     - ".github/workflows/"
@@ -282,12 +289,22 @@ changelog:
 nf_schema:
   skippable_paths:
     - "subworkflows/nf-core/utils_nfschema_plugin"
+    - "nextflow_schema.json"
+    - "assets/schema_input.json"
+    - "assets/samplesheet.csv"
   short_description: "Use nf-schema"
   description: "Use the nf-schema Nextflow plugin for this pipeline."
   help_text: |
     [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema.
     It also provides helper functionality to create help messages, get a summary
     of changed parameters and validate and convert a samplesheet to a channel.
+  linting:
+    files_exist:
+      - "nextflow_schema.json"
+    schema_params: False
+    schema_lint: False
+    schema_description: False
+    nextflow_config: False
   nfcore_pipelines: True
   custom_pipelines: True
 license:

nf_core/pipelines/create/utils.py

@@ -37,7 +37,7 @@ def init_context(value: Dict[str, Any]) -> Iterator[None]:
 NFCORE_PIPELINE_GLOBAL: bool = True
 
 # YAML file describing template features
-features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml"
+features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "template_features.yml"
 
 
 class CreateConfig(NFCoreTemplateConfig):