Look in Temp directories for some of the files we have historically

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

diff --git a/htsworkflow/pipelines/eland.py b/htsworkflow/pipelines/eland.py
index 864f8ca4454eb93c8ffde3f83aaac51dede72252..05563a1a2cb5ba455c7a4b360c955c60eb630738 100644 (file)
--- a/htsworkflow/pipelines/eland.py
+++ b/htsworkflow/pipelines/eland.py
@@ -316,10 +316,13 @@ def check_for_eland_file(basedir, pattern, lane_id, end):
 def eland(basedir, gerald=None, genome_maps=None):
     e = ELAND()
 
-    #file_list = glob(os.path.join(basedir, "*_eland_result.txt"))
-    #if len(file_list) == 0:
-    #    # lets handle compressed eland files too
-    #    file_list = glob(os.path.join(basedir, "*_eland_result.txt.bz2"))
+    # if there is a basedir/Temp change basedir to point to the temp
+    # directory, as 1.1rc1 moves most of the files we've historically
+    # cared about to that subdirectory.
+    # we should look into what the official 'result' files are.
+    basedir_temp = os.path.join(basedir, 'Temp')
+    if os.path.isdir(basedir_temp):
+        basedir = basedir_temp
 
     lane_ids = range(1,9)
     ends = [None, 1, 2]