Merge pull request #1517 from fabianegli/fabianegli-remove-graphviz-d…

…ependency

revert to single dag.file file format for linting

CHANGELOG.md

@@ -2,8 +2,6 @@
 
 ## v2.4dev
 
-This patch release to removes the Graphviz dependency from default pipeline template by setting the defaul DAG format to HTML. To keep the previous behaviour, the "dag.file" file extension needs to be changed to ".svg" in the nextflow.config.
-
 ### Template
 
 - Set the default DAG graphic output to HTML to have a default that does not depend on Graphviz being installed on the host system ([#1512](https://github.com/nf-core/tools/pull/1512)).

nf_core/lint/nextflow_config.py

@@ -229,14 +229,11 @@ def nextflow_config(self):
 
     # Check that the DAG filename ends in ``.svg``
     if "dag.file" in self.nf_config:
-        _, dag_file_suffix = os.path.splitext(self.nf_config["dag.file"].strip("'\""))
-        allowed_dag_file_suffixes = [".dot", ".html", ".pdf", ".png", ".svg", ".gexf"]
-        if dag_file_suffix in allowed_dag_file_suffixes:
-            passed.append(f"Config ``dag.file`` ended with ``.{dag_file_suffix}``")
+        default_dag_format = ".html"
+        if self.nf_config["dag.file"].strip("'\"").endswith(default_dag_format):
+            passed.append(f"Config ``dag.file`` ended with ``{default_dag_format}``")
         else:
-            failed.append(
-                f"Config ``dag.file`` ended with ``.{dag_file_suffix}`` but needs to be one of {allowed_dag_file_suffixes!r}"
-            )
+            failed.append(f"Config ``dag.file`` did not end with ``{default_dag_format}``")
 
     # Check that the minimum nextflowVersion is set properly
     if "manifest.nextflowVersion" in self.nf_config: