nf-core · KevinMenden · Apr 16, 2021 · Apr 16, 2021 · Apr 16, 2021 · Apr 16, 2021
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@
 * Added a timestamp to the trace + timetime + report + dag filenames to fix overwrite issue on AWS
 * Rewrite the `params_summary_log()` function to properly ignore unset params and have nicer formatting [[#971](https://github.com/nf-core/tools/issues/971)]
 * Fix overly strict `--max_time` formatting regex in template schema [[#973](https://github.com/nf-core/tools/issues/973)]
+* Added `tool_name_underscore` to the module template to allow TOOL_SUBTOOL in `main.nf` [[#1011](https://github.com/nf-core/tools/issues/1011)]
 * Convert `d` to `day` in the `cleanParameters` function to make Duration objects like `2d` pass the validation [[#858](https://github.com/nf-core/tools/issues/858)]
 
 ## [v1.13.3 - Copper Crocodile Resurrection :crocodile:](https://github.com/nf-core/tools/releases/tag/1.13.2) - [2021-03-24]

diff --git a/nf_core/module-template/software/functions.nf b/nf_core/module-template/software/functions.nf
@@ -67,4 +67,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}
diff --git a/nf_core/module-template/software/main.nf b/nf_core/module-template/software/main.nf
@@ -20,7 +20,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 options        = initOptions(params.options)
 
-process {{ tool_name|upper }} {
+process {{ tool_name_underscore|upper }} {
     tag {{ '"$meta.id"' if has_meta else "'$bam'" }}
     label '{{ process_label }}'
     publishDir "${params.outdir}",

diff --git a/nf_core/module-template/software/meta.yml b/nf_core/module-template/software/meta.yml
@@ -1,4 +1,4 @@
-name: {{ tool_name }}
+name: {{ tool_name_underscore }}
 ## TODO nf-core: Add a description of the module and list keywords
 description: write your description here
 keywords:

diff --git a/nf_core/module-template/tests/main.nf b/nf_core/module-template/tests/main.nf
@@ -2,15 +2,15 @@
 
 nextflow.enable.dsl = 2
 
-include { {{ tool_name|upper }} } from '../../../{{ "../" if subtool else "" }}software/{{ tool_dir }}/main.nf' addParams( options: [:] )
+include { {{ tool_name_underscore|upper }} } from '../../../{{ "../" if subtool else "" }}software/{{ tool_dir }}/main.nf' addParams( options: [:] )
 
-workflow test_{{ tool_name }} {
+workflow test_{{ tool_name_underscore }} {
     {% if has_meta %}
     input = [ [ id:'test', single_end:false ], // meta map
               file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
     {%- else %}
     input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
     {%- endif %}
 
-    {{ tool_name|upper }} ( input )
+    {{ tool_name_underscore|upper }} ( input )
 }
diff --git a/nf_core/module-template/tests/test.yml b/nf_core/module-template/tests/test.yml
@@ -1,7 +1,7 @@
 ## TODO nf-core: Please run the following command to build this file:
 #                nf-core modules create-test-yml {{ tool }}{%- if subtool %}/{{ subtool }}{%- endif %}
 - name: {{ tool }}{{ ' '+subtool if subtool else '' }}
-  command: nextflow run ./tests/software/{{ tool_dir }} -entry test_{{ tool_name }} -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/{{ tool_dir }} -entry test_{{ tool_name_underscore }} -c tests/config/nextflow.config
   tags:
     - {{ tool }}
     {%- if subtool %}

diff --git a/nf_core/modules/create.py b/nf_core/modules/create.py
@@ -33,9 +33,8 @@ def __init__(
         self.process_label = process_label
         self.has_meta = has_meta
         self.force_overwrite = force
-
-        self.tool_conda_name = conda_name
         self.subtool = None
+        self.tool_conda_name = conda_name
         self.tool_licence = None
         self.repo_type = None
         self.tool_licence = ""
@@ -116,6 +115,8 @@ def create(self):
             self.tool_name = f"{self.tool}/{self.subtool}"
             self.tool_dir = os.path.join(self.tool, self.subtool)
 
+        self.tool_name_underscore = self.tool_name.replace("/", "_")
+
         # Check existance of directories early for fast-fail
         self.file_paths = self.get_module_dirs()
-Original file line number
+Diff line change
@@ Expand Up / @@ -67,4 +67,4 @@ def saveFiles(Map args) { @@
                 return "${getPathFromList(path_list)}/$args.filename"
             }
         }
-    }
+    }