Report missing directory names to help diagnose sequence scanning problems

diff --git a/htsworkflow/pipelines/sequences.py b/htsworkflow/pipelines/sequences.py
index 84bafbfb4af38d95aa68e25083650747d0c73df4..24cf88488525844cef7ee0f4cffe9454924a8f4d 100644 (file)
--- a/htsworkflow/pipelines/sequences.py
+++ b/htsworkflow/pipelines/sequences.py
@@ -216,6 +216,10 @@ def scan_for_sequences(dirs):
     sequences = []
     for d in dirs:
         logging.info("Scanning %s for sequences" % (d,))
+        if not os.path.exists(d):
+            logging.warn("Flowcell directory %s does not exist" % (d,))
+            continue
+        
         for path, dirname, filenames in os.walk(d):
             for f in filenames:
                 seq = None