fix DAG building when checkpoints are included

Author: WardDeb

bioproject/{{ cookiecutter.project_slug }}/scripts/workflow_functions.py

@@ -127,7 +127,13 @@ def runSmk(smk, configfile, wdir, profile):
     )
     _stdout, _stderr = rg.communicate()
     # Some snakemake versions still print that 'building' line in stdout. Get rid of it.
-    _stdout = _stdout.decode('utf-8').replace('Building DAG of jobs...\n', '').encode()
+    _stdout = (
+        _stdout
+            .decode('utf-8')
+            .replace('Building DAG of jobs...\n', '')
+            .replace("Updating checkpoint dependencies.\n", "")
+            .encode()
+    )
 
     if rg.returncode != 0:
         print(f"[bold red]Dryrun failed - return {rg.returncode}[/bold red]")