style: yaml => yml

nf_core/lint/files_exist.py

@@ -62,7 +62,7 @@ def files_exist(self):
     .. code-block:: bash
 
         main.nf
-        assets/multiqc_config.yaml
+        assets/multiqc_config.yml
         conf/base.config
         conf/igenomes.config
         .github/workflows/awstest.yml
@@ -144,7 +144,7 @@ def files_exist(self):
 
     files_warn = [
         ["main.nf"],
-        [os.path.join("assets", "multiqc_config.yaml")],
+        [os.path.join("assets", "multiqc_config.yml")],
         [os.path.join("conf", "base.config")],
         [os.path.join("conf", "igenomes.config")],
         [os.path.join(".github", "workflows", "awstest.yml")],

nf_core/lint/multiqc_config.py

@@ -25,11 +25,11 @@ def multiqc_config(self):
     warned = []
     failed = []
 
-    fn = os.path.join(self.wf_path, "assets", "multiqc_config.yaml")
+    fn = os.path.join(self.wf_path, "assets", "multiqc_config.yml")
 
     # Return a failed status if we can't find the file
     if not os.path.isfile(fn):
-        return {"ignored": ["'assets/multiqc_config.yaml' not found"]}
+        return {"ignored": ["'assets/multiqc_config.yml' not found"]}
 
     try:
         with open(fn, "r") as fh:
@@ -61,9 +61,9 @@ def multiqc_config(self):
             orders.values()
         ), f"Section software_versions should have the second lowest order"
     except (AssertionError, KeyError, TypeError) as e:
-        failed.append(f"'assets/multiqc_config.yaml' does not meet requirements: {e}")
+        failed.append(f"'assets/multiqc_config.yml' does not meet requirements: {e}")
     else:
-        passed.append("'assets/multiqc_config.yaml' follows the ordering scheme of the minimally required plugins.")
+        passed.append("'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.")
 
     # Check that the minimum plugins exist and are coming first in the summary
     try:
@@ -73,17 +73,17 @@ def multiqc_config(self):
             == f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}" target="_blank">nf-core/{self.pipeline_name}</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/{self.pipeline_name}" target="_blank">documentation</a>.'
         )
     except (AssertionError, KeyError, TypeError):
-        failed.append("'assets/multiqc_config.yaml' does not contain a matching 'report_comment'.")
+        failed.append("'assets/multiqc_config.yml' does not contain a matching 'report_comment'.")
     else:
-        passed.append("'assets/multiqc_config.yaml' contains a matching 'report_comment'.")
+        passed.append("'assets/multiqc_config.yml' contains a matching 'report_comment'.")
 
     # Check that export_plots is activated
     try:
         assert "export_plots" in mqc_yml
         assert mqc_yml["export_plots"] == True
     except (AssertionError, KeyError, TypeError):
-        failed.append("'assets/multiqc_config.yaml' does not contain 'export_plots: true'.")
+        failed.append("'assets/multiqc_config.yml' does not contain 'export_plots: true'.")
     else:
-        passed.append("'assets/multiqc_config.yaml' contains 'export_plots: true'.")
+        passed.append("'assets/multiqc_config.yml' contains 'export_plots: true'.")
 
     return {"passed": passed, "failed": failed}

nf_core/pipeline-template/.github/CONTRIBUTING.md

@@ -73,7 +73,7 @@ If you wish to contribute a new step, please use the following coding standards:
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
-9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values

nf_core/pipeline-template/workflows/pipeline.nf

@@ -23,7 +23,7 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
+ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
 ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
 
 /*