Parse runfolders generated with IPAR 1.3 and pipeline 1.3.2

[htsworkflow.git] / htsworkflow / pipelines / test / simulate_runfolder.py

diff --git a/htsworkflow/pipelines/test/simulate_runfolder.py b/htsworkflow/pipelines/test/simulate_runfolder.py
index 72c1a1a5958ffc9dd93034a0434f13938954d8e6..5354cfbac1e691e97e67caed9e35d23e52cfc493 100644 (file)
--- a/htsworkflow/pipelines/test/simulate_runfolder.py
+++ b/htsworkflow/pipelines/test/simulate_runfolder.py
@@ -3,6 +3,7 @@ Create simulated solexa/illumina runfolders for testing
 """
 
 import os
+import shutil
 
 def make_firecrest_dir(data_dir, version="1.9.2", start=1, stop=37):
     firecrest_dir = os.path.join(data_dir, 
@@ -1899,6 +1900,13 @@ def make_summary_paired_htm(gerald_dir):
     f.write(summary_htm)
     f.close()
 
+def make_summary_ipar130_htm(gerald_dir):
+     test_dir = os.path.split(__file__)[0]
+     testdata_dir = os.path.join(test_dir, 'testdata')
+     summary_htm = os.path.join(testdata_dir, 'Summary-ipar130.htm')
+     dest = os.path.join(gerald_dir, 'Summary.htm')
+     shutil.copy(summary_htm, dest)
+
 def make_eland_results(gerald_dir):
     eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759    ACATAGNCACAGACATAAACATAGACATAGAC U0      1       1       3       chrUextra.fa    28189829        R       D.
 >HWI-EAS229_24_207BTAAXX:1:7:205:842    AAACAANNCTCCCAAACACGTAAACTGGAAAA  U1      0       1       0       chr2L.fa        8796855 R       DD      24T