Put the -c back for the test pipeline nextflow.config

Avoid needing to change loads of module files due to the template update. See #1562 (comment)
nf-core · May 12, 2022 · d61a51d · d61a51d
1 parent 74441fd
commit d61a51d
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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/modules/{{ tool_dir }} -entry test_{{ tool_name_underscore }} -c ./tests/config/nextflow.config
+  command: nextflow run ./tests/modules/{{ tool_dir }} -entry test_{{ tool_name_underscore }} -c ./tests/config/nextflow.config -c ./tests/modules/{{ tool_dir }}/nextflow.config
   tags:
     - "{{ tool }}"
     # {%- if subtool %}

diff --git a/nf_core/modules/test_yml_builder.py b/nf_core/modules/test_yml_builder.py
@@ -164,7 +164,9 @@ def build_single_test(self, entry_point):
                 ep_test["name"] = rich.prompt.Prompt.ask("[violet]Test name", default=default_val).strip()
 
         while ep_test["command"] == "":
-            default_val = f"nextflow run ./tests/modules/{self.module_name} -entry {entry_point} -c ./tests/config/nextflow.config"
+            # Don't think we need the last `-c` flag, but keeping to avoid having to update 100s modules.
+            # See https://github.com/nf-core/tools/issues/1562
+            default_val = f"nextflow run ./tests/modules/{self.module_name} -entry {entry_point} -c ./tests/config/nextflow.config  -c ./tests/modules/{self.module_name}/nextflow.config"
             if self.no_prompts:
                 ep_test["command"] = default_val
             else: