fixed bug nf-core#1011

CHANGELOG.md

@@ -17,6 +17,7 @@
 * 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)]
 
 ## [v1.13.3 - Copper Crocodile Resurrection :crocodile:](https://github.com/nf-core/tools/releases/tag/1.13.2) - [2021-03-24]
 

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}",

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()