X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=htsworkflow%2Fpipelines%2Fsrf2fastq.py;h=3131fddc7e6edef563a953081f2f9f97e1ff37d2;hb=2045ea9a60f315dabf1fb190713dda237c7a6b0b;hp=adaa1b2dfe4efcfcd5186bfa86a350ce093de88e;hpb=e39a73a02997e38a6dbf7797c5f657793e9c7059;p=htsworkflow.git

diff --git a/htsworkflow/pipelines/srf2fastq.py b/htsworkflow/pipelines/srf2fastq.py
index adaa1b2..3131fdd 100755
--- a/htsworkflow/pipelines/srf2fastq.py
+++ b/htsworkflow/pipelines/srf2fastq.py
@@ -44,7 +44,7 @@ def main(cmdline=None):
     
     # open the srf, fastq, or compressed fastq
     if is_srf(args[0]):
-        source = srf_open(args[0])
+        source = srf_open(args[0], opts.cnf1)
     else:
         source = autoopen(args[0])
 
@@ -77,6 +77,8 @@ You can also force the flowcell ID to be added to the header.""")
                       help="show information about what we're doing.")
     parser.add_option('--version', default=False, action="store_true",
                       help="Report software version")
+    parser.add_option('--cnf1', default=False, action="store_true",
+                      help="Force cnf1 mode in srf2fastq")
     return parser
 
 
@@ -85,7 +87,7 @@ def srf_open(filename, cnf1=False):
     Make a stream from srf file using srf2fastq
     """
     cmd = ['srf2fastq']
-    if is_cnf1(filename):
+    if cnf1 or is_cnf1(filename):
         cmd.append('-c')
     cmd.append(filename)