Replace nf-core with org in module templates #2069
Conversation
Codecov Report
@@ Coverage Diff @@
## dev #2069 +/- ##
=======================================
Coverage 67.66% 67.66%
=======================================
Files 43 43
Lines 5555 5555
=======================================
Hits 3759 3759
Misses 1796 1796 Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here. |
…tools into fix-module-template-org
| @@ -1,7 +1,7 @@ | |||
| ## TODO nf-core: Please run the following command to build this file: | |||
| # nf-core subworkflows create-test-yml {{ subworkflow_name_underscore }} | |||
| - name: "{{ subworkflow_name }}" | |||
| command: nextflow run ./tests/subworkflows/nf-core/{{ subworkflow_dir }} -entry test_{{ subworkflow_name }} -c ./tests/config/nextflow.config | |||
| command: nextflow run ./tests/subworkflows/{{ org }}/{{ subworkflow_dir }} -entry test_{{ subworkflow_name }} -c ./tests/config/nextflow.config | |||
There was a problem hiding this comment.
Why do we not pass the nextflow.config that sits alongside the test main.nf explicitly here as we do for modules?
There was a problem hiding this comment.
It's not required, we still have it in modules to avoid changing too many files (see #1562), but now that we are starting fresh with subworkflows we don't need to add it.
There was a problem hiding this comment.
What exactly isn't required? We still create a local config file in tests/subworkflows/<org>/<TOOL>
There was a problem hiding this comment.
Sorry I didn't explain good 😅 We don't need to pass the path of this file explicitly, as it's located in the same folder as main.nf, it's taken into account by Nextflow by default.
Make sure
org_pathis inserted into templates instead of hard-codednf-corePR checklist
CHANGELOG.mdis updateddocsis updated