Add --empty-template flag for creating modules

CHANGELOG.md

@@ -11,6 +11,8 @@
 
 ### Modules
 
+- Add an `--empty-template` option to create a module without TODO statements or examples ([#2175](https://github.com/nf-core/tools/pull/2175))
+
 ### Subworkflows
 
 ### General

nf_core/__main__.py

@@ -678,8 +678,16 @@ def remove(ctx, dir, tool):
 @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite any files if they already exist")
 @click.option("-c", "--conda-name", type=str, default=None, help="Name of the conda package to use")
 @click.option("-p", "--conda-package-version", type=str, default=None, help="Version of conda package to use")
-@click.option("-i", "--minimal", is_flag=True, default=False, help="Create a minimal version of the template")
-def create_module(ctx, tool, dir, author, label, meta, no_meta, force, conda_name, conda_package_version, minimal):
+@click.option(
+    "-i",
+    "--empty-template",
+    is_flag=True,
+    default=False,
+    help="Create a version of the template without TODOs or examples",
+)
+def create_module(
+    ctx, tool, dir, author, label, meta, no_meta, force, conda_name, conda_package_version, empty_template
+):
     """
     Create a new DSL2 module from the nf-core template.
 
@@ -701,7 +709,7 @@ def create_module(ctx, tool, dir, author, label, meta, no_meta, force, conda_nam
     # Run function
     try:
         module_create = nf_core.modules.ModuleCreate(
-            dir, tool, author, label, has_meta, force, conda_name, conda_package_version, minimal
+            dir, tool, author, label, has_meta, force, conda_name, conda_package_version, empty_template
         )
         module_create.create()
     except UserWarning as e:

nf_core/components/create.py

@@ -36,7 +36,7 @@ def __init__(
         force=False,
         conda_name=None,
         conda_version=None,
-        minimal=False,
+        empty_template=False,
     ):
         super().__init__(component_type, directory)
         self.directory = directory
@@ -57,7 +57,7 @@ def __init__(
         self.singularity_container = None
         self.docker_container = None
         self.file_paths = {}
-        self.not_minimal = not minimal
+        self.not_empty_template = not empty_template
 
     def create(self):
         """

nf_core/module-template/modules/main.nf

@@ -1,4 +1,4 @@
-{%- if not_minimal -%}
+{%- if not_empty_template -%}
 // TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
 //               https://github.com/nf-core/modules/tree/master/modules/nf-core/
 //               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
@@ -21,7 +21,7 @@ process {{ component_name_underscore|upper }} {
     tag {{ '"$meta.id"' if has_meta else "'$bam'" }}
     label '{{ process_label }}'
 
-    {% if not_minimal -%}
+    {% if not_empty_template -%}
     // TODO nf-core: List required Conda package(s).
     //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
@@ -33,7 +33,7 @@ process {{ component_name_underscore|upper }} {
         '{{ docker_container if docker_container else 'quay.io/biocontainers/YOUR-TOOL-HERE' }}' }"
 
     input:
-    {% if not_minimal -%}
+    {% if not_empty_template -%}
     // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
     //               MUST be provided as an input via a Groovy Map called "meta".
     //               This information may not be required in some instances e.g. indexing reference genome files:
@@ -46,13 +46,13 @@ process {{ component_name_underscore|upper }} {
     {%- endif %}
 
     output:
-    {% if not_minimal -%}
+    {% if not_empty_template -%}
     // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
     {{ 'tuple val(meta), path("*.bam")' if has_meta else 'path "*.bam"' }}, emit: bam
     {%- else -%}
     {{ 'tuple val(meta), path("*")' if has_meta else 'path "*"' }}, emit: output
     {%- endif %}
-    {% if not_minimal -%}
+    {% if not_empty_template -%}
     // TODO nf-core: List additional required output channels/values here
     {%- endif %}
     path "versions.yml"           , emit: versions
@@ -65,7 +65,7 @@ process {{ component_name_underscore|upper }} {
     {% if has_meta -%}
     def prefix = task.ext.prefix ?: "${meta.id}"
     {%- endif %}
-    {% if not_minimal -%}
+    {% if not_empty_template -%}
     // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
     //               If the software is unable to output a version number on the command-line then it can be manually specified
     //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
@@ -77,7 +77,7 @@ process {{ component_name_underscore|upper }} {
     // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
     {%- endif %}
     """
-    {% if not_minimal -%}
+    {% if not_empty_template -%}
     samtools \\
         sort \\
         $args \\

nf_core/module-template/modules/meta.yml

@@ -1,13 +1,13 @@
 name: "{{ component_name_underscore }}"
-{% if not_minimal -%}
+{% if not_empty_template -%}
 ## TODO nf-core: Add a description of the module and list keywords
 {%- endif -%}
 description: write your description here
 keywords:
   - sort
 tools:
   - "{{ component }}":
-      {% if not_minimal -%}
+      {% if not_empty_template -%}
       ## TODO nf-core: Add a description and other details for the software below
       {% endif -%}
       description: "{{ tool_description }}"
@@ -17,7 +17,7 @@ tools:
       doi: ""
       licence: "{{ tool_licence }}"
 
-{% if not_minimal -%}
+{% if not_empty_template -%}
 ## TODO nf-core: Add a description of all of the variables used as input
 {% endif -%}
 input:
@@ -28,15 +28,15 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   {% endif %}
-  {% if not_minimal -%}
+  {% if not_empty_template -%}
   ## TODO nf-core: Delete / customise this example input
   {%- endif %}
-  - {{ 'bam:' if not_minimal else "input:" }}
+  - {{ 'bam:' if not_empty_template else "input:" }}
     type: file
-    description: {{ 'Sorted BAM/CRAM/SAM file' if not_minimal else "" }}
-    pattern: {{ '"*.{bam,cram,sam}"' if not_minimal else "" }}
+    description: {{ 'Sorted BAM/CRAM/SAM file' if not_empty_template else "" }}
+    pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }}
 
-{% if not_minimal -%}
+{% if not_empty_template -%}
 ## TODO nf-core: Add a description of all of the variables used as output
 {% endif -%}
 output:
@@ -51,13 +51,13 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  {% if not_minimal -%}
+  {% if not_empty_template -%}
   ## TODO nf-core: Delete / customise this example output
   {%- endif %}
-  - {{ 'bam:' if not_minimal else "output:" }}
+  - {{ 'bam:' if not_empty_template else "output:" }}
     type: file
-    description: {{ 'Sorted BAM/CRAM/SAM file' if not_minimal else "" }}
-    pattern: {{ '"*.{bam,cram,sam}"' if not_minimal else "" }}
+    description: {{ 'Sorted BAM/CRAM/SAM file' if not_empty_template else "" }}
+    pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }}
 
 authors:
   - "{{ author }}"

nf_core/module-template/tests/test.yml

@@ -1,4 +1,4 @@
-{%- if not_minimal -%}
+{%- if not_empty_template -%}
 ## TODO nf-core: Please run the following command to build this file:
 #                nf-core modules create-test-yml {{ tool }}{%- if subtool %}/{{ subtool }}{%- endif %}
 {% endif -%}
@@ -8,7 +8,7 @@
     - "{{ component }}{% if subtool -%}"
     - "{{ component }}/{{ subtool }}{%- endif %}"
   files:
-    {% if not_minimal -%}
+    {% if not_empty_template -%}
     - path: "output/{{ component }}/test.bam"
       md5sum: e667c7caad0bc4b7ac383fd023c654fc
     - path: "output/{{ component }}/versions.yml"

nf_core/modules/create.py

@@ -16,7 +16,7 @@ def __init__(
         force=False,
         conda_name=None,
         conda_version=None,
-        minimal=False,
+        empty_template=False,
     ):
         super().__init__(
             "modules",
@@ -28,5 +28,5 @@ def __init__(
             force,
             conda_name,
             conda_version,
-            minimal,
+            empty_template,
         )