From d61a51d13dd7ddbcba326a1a1d5efccd09399914 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 12 May 2022 15:32:18 +0200
Subject: [PATCH] Put the -c back for the test pipeline nextflow.config

Avoid needing to change loads of module files due to the template update.
See https://github.com/nf-core/tools/issues/1562#issuecomment-1124994152
---
 nf_core/module-template/tests/test.yml | 2 +-
 nf_core/modules/test_yml_builder.py    | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/nf_core/module-template/tests/test.yml b/nf_core/module-template/tests/test.yml
index c1782107a..b0eb64584 100644
--- 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
index f96b3d6ca..4b8537159 100644
--- 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: