Update summary script to read from the GERALD Summary.xml file

[htsworkflow.git] / htsworkflow / pipelines / gerald.py

diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py
index 980c6616231623d1e0677bbdb2306052241ea2a4..35bc037f3c2db7c5fa867e0270be607eb1f8d4fd 100644 (file)
--- a/htsworkflow/pipelines/gerald.py
+++ b/htsworkflow/pipelines/gerald.py
@@ -194,8 +194,12 @@ def gerald(pathname):
     g.tree = ElementTree.parse(config_pathname).getroot()
 
     # parse Summary.htm file
-    logging.info("Parsing Summary.htm")
-    summary_pathname = os.path.join(g.pathname, 'Summary.htm')
+    summary_pathname = os.path.join(g.pathname, 'Summary.xml')
+    if os.path.exists(summary_pathname):
+        logging.info("Parsing Summary.xml")
+    else:
+        summary_pathname = os.path.join(g.pathname, 'Summary.htm')
+        logging.info("Parsing Summary.htm")
     g.summary = Summary(summary_pathname)
     # parse eland files
     g.eland_results = eland(g.pathname, g)