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Make module template and test_yml_builder default commands match. #1568

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merged 3 commits into from
May 12, 2022
Merged

Make module template and test_yml_builder default commands match. #1568

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2eea6d6
Make module template and test_yml_builder default commands match.
ewels May 12, 2022
74441fd
Changelog
ewels May 12, 2022
d61a51d
Put the -c back for the test pipeline nextflow.config
ewels May 12, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,7 @@
- Removed retry strategy for AWS tests CI, as Nextflow now handles spot instance retries itself
- Add `.prettierignore` file to stop Prettier linting tests from running over test files
- Add actions workflow to respond to `@nf-core-bot fix linting` comments on pipeline PRs
- Made module template test command match the default used in `nf-core modules create-test-yml` ([#1562](https://github.com/nf-core/tools/issues/1562))

### General

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2 changes: 1 addition & 1 deletion nf_core/module-template/tests/test.yml
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@@ -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 -c ./tests/modules/{{ tool_dir }}/nextflow.config
command: nextflow run ./tests/modules/{{ tool_dir }} -entry test_{{ tool_name_underscore }} -c ./tests/config/nextflow.config
tags:
- "{{ tool }}"
# {%- if subtool %}
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4 changes: 1 addition & 3 deletions nf_core/modules/test_yml_builder.py
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Expand Up @@ -164,9 +164,7 @@ 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"
)
default_val = f"nextflow run ./tests/modules/{self.module_name} -entry {entry_point} -c ./tests/config/nextflow.config"
if self.no_prompts:
ep_test["command"] = default_val
else:
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