Merge pull request #2225 from nf-core/schema-lint-argument

CHANGELOG.md

@@ -14,6 +14,7 @@
 ### Linting
 
 - Read module lint configuration from `.nf-core.yml`, not `.nf-core-lint.yml` ([#2221](https://github.com/nf-core/tools/pull/2221))
+- `nf-core schema lint` now defaults to linting `nextflow_schema.json` if no filename is provided ([#2225](https://github.com/nf-core/tools/pull/2225))
 
 ### Modules
 

README.md

@@ -634,13 +634,13 @@ It's important to change the default value of a parameter in the `nextflow.confi
 The pipeline schema is linted as part of the main pipeline `nf-core lint` command,
 however sometimes it can be useful to quickly check the syntax of the JSONSchema without running a full lint run.
 
-Usage is `nf-core schema lint <schema>`, eg:
+Usage is `nf-core schema lint <schema>` (defaulting to `nextflow_schema.json`), eg:
 
 <!-- RICH-CODEX
 working_dir: tmp/nf-core-nextbigthing
 -->
 
-![`nf-core schema lint nextflow_schema.json`](docs/images/nf-core-schema-lint.svg)
+![`nf-core schema lint`](docs/images/nf-core-schema-lint.svg)
 
 ## Bumping a pipeline version number
 

nf_core/__main__.py

@@ -1398,7 +1398,7 @@ def build(dir, no_prompts, web_only, url):
 
 # nf-core schema lint
 @schema.command()
-@click.argument("schema_path", type=click.Path(exists=True), required=True, metavar="<pipeline schema>")
+@click.argument("schema_path", type=click.Path(exists=True), default="nextflow_schema.json", metavar="<pipeline schema>")
 def lint(schema_path):
     """
     Check that a given pipeline schema is valid.
@@ -1408,6 +1408,8 @@ def lint(schema_path):
 
     This function runs as part of the nf-core lint command, this is a convenience
     command that does just the schema linting nice and quickly.
+
+    If no schema path is provided, "nextflow_schema.json" will be used (if it exists).
     """
     schema_obj = nf_core.schema.PipelineSchema()
     try:

tests/test_cli.py

@@ -350,3 +350,20 @@ def test_lint_log_user_warning(self, mock_lint, mock_is_pipeline):
         assert result.exit_code == 1
         assert error_txt in captured_logs.output[-1]
         assert captured_logs.records[-1].levelname == "ERROR"
+
+    @mock.patch("nf_core.schema.PipelineSchema.get_schema_path")
+    def test_schema_lint(self, mock_get_schema_path):
+        """Test nf-core schema lint defaults to nextflow_schema.json"""
+        cmd = ["schema", "lint"]
+        result = self.invoke_cli(cmd)
+        assert mock_get_schema_path.called_with("nextflow_schema.json")
+        assert "nextflow_schema.json" in result.output
+
+    @mock.patch("nf_core.schema.PipelineSchema.get_schema_path")
+    def test_schema_lint_filename(self, mock_get_schema_path):
+        """Test nf-core schema lint accepts a filename"""
+        cmd = ["schema", "lint", "some_other_filename"]
+        result = self.invoke_cli(cmd)
+        assert mock_get_schema_path.called_with("some_other_filename")
+        assert "some_other_filename" in result.output
+        assert "nextflow_schema.json" not in result.output