Merge pull request #1512 from fabianegli/fabianegli-remove-graphviz-d…

…ependency

Remove the graphviz dependency from nf-core

CHANGELOG.md

@@ -2,8 +2,11 @@
 
 ## 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)).
 - Fix bug in pipeline readme logo URL
 - Fix Prettier formatting bug in completion email HTML template ([#1509](https://github.com/nf-core/tools/issues/1509))
 - Removed retry strategy for AWS tests CI, as Nextflow now handles spot instance retries itself

nf_core/lint/nextflow_config.py

@@ -229,10 +229,14 @@ def nextflow_config(self):
 
     # Check that the DAG filename ends in ``.svg``
     if "dag.file" in self.nf_config:
-        if self.nf_config["dag.file"].strip("'\"").endswith(".svg"):
-            passed.append("Config ``dag.file`` ended with ``.svg``")
+        _, 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}``")
         else:
-            failed.append("Config ``dag.file`` did not end with ``.svg``")
+            failed.append(
+                f"Config ``dag.file`` ended with ``.{dag_file_suffix}`` but needs to be one of {allowed_dag_file_suffixes!r}"
+            )
 
     # Check that the minimum nextflowVersion is set properly
     if "manifest.nextflowVersion" in self.nf_config:

nf_core/pipeline-template/nextflow.config

@@ -159,7 +159,7 @@ trace {
 }
 dag {
     enabled = true
-    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
+    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
 }
 
 manifest {