fix#3

README.md

@@ -60,7 +60,7 @@ Please follow these instruction:
 
 **NOTE: You need to install the third-party tools to work with pyrpipe. We recomend installing these through [bioconda](https://bioconda.github.io/) where possible. 
 A recommended environment file, using python 3.7, is given [here](https://github.com/urmi-21/pyrpipe/blob/master/tests/test_environment.yml).
-It is best to [share your conda environment files](https://stackoverflow.com/questions/41274007/anaconda-export-environment-file) with pyrpipe scripts to ensure reproducibility**
+It is best to [share your conda environment files](https://stackoverflow.com/questions/41274007/anaconda-export-environment-file) with pyrpipe scripts to ensure reproducibility.**
 
 ### Install latest stable version
 

pyrpipe/assembly.py

@@ -117,7 +117,7 @@ def perform_assembly(self,bam_file,out_dir="",out_suffix="_stringtie",overwrite=
         else:
             return ""
 
-    def stringtie_merge(self,*args,out_suffix="_stringtieMerge",overwrite=True,verbose=False,quiet=False,logs=True,objectid="NA",**kwargs):
+    def stringtie_merge(self,*args,out_dir=None,out_suffix="_stringtieMerge",overwrite=True,verbose=False,quiet=False,logs=True,objectid="NA",**kwargs):
         """Function to run stringtie merge.
         
         Parameters
@@ -150,7 +150,10 @@ def stringtie_merge(self,*args,out_suffix="_stringtieMerge",overwrite=True,verbo
 
         #create path to output sam file
         fname=pu.get_file_basename(args[0])
-        out_dir=pu.get_file_directory(args[0])
+
+        if not out_dir:
+            out_dir=pu.get_file_directory(args[0])
+
         out_gtf_file=os.path.join(out_dir,fname+out_suffix+".gtf")
 
         if not overwrite: