Merge pull request #153 from Daniel-VM/dev

Fixed `files_unchanged` section in `.nf-core.yml` to allow a proper linting test.

.github/CONTRIBUTING.md

@@ -26,7 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
-You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile.
+You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
+
+```bash
+nf-test test --profile debug,test,docker --verbose
+```
 
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
@@ -47,14 +51,6 @@ Each `nf-core` pipeline should be set up with a minimal set of test-data.
 If there are any failures then the automated tests fail.
 These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
 
-You can run pipeline tests with the following command:
-
-```bash
-nextflow run nf-core/bacass \
-  -profile <test,test_long,test_hybrid,...>,<docker/singularity/.../institute> \
-  --outdir <OUTDIR>
-```
-
 ## Patch
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/baca
 - [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.nf-core.yml

@@ -2,9 +2,6 @@ repository_type: pipeline
 lint:
   files_exist:
     - conf/igenomes.config
-  files_unchanged:
-    - .github/CONTRIBUTING.md
-    - .github/PULL_REQUEST_TEMPLATE.md
   nextflow_config:
     - config_defaults:
         - params.dfast_config

CHANGELOG.md

@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#153](https://github.com/nf-core/bacass/pull/153) Update `.nf-core.yml` to fix files_unchanged section for accurate linting checks.
+
 ### `Dependencies`
 
 ### `Deprecated`