From: Diane Trout <diane@caltech.edu>
Date: Mon, 9 May 2011 21:53:17 +0000 (-0700)
Subject: Report missing directory names to help diagnose sequence scanning problems
X-Git-Tag: 0.5.2~40^2~2
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=2f98a5921d879ac4d2c23699b3d67aa926504b24

Report missing directory names to help diagnose sequence scanning problems
---

diff --git a/htsworkflow/pipelines/sequences.py b/htsworkflow/pipelines/sequences.py
index 84bafbf..24cf884 100644
--- 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