updateRM

examples/Human_annotation_snakemake/README.md

@@ -1,3 +1,12 @@
+# Introduction
+
+## Integrating pyrpipe scripts within a workflow management system (Snakemake)
+We embedded pyrpipe into the Snakemake workflow management system, using it to download human RNA-Seq data with SRAtools, 
+quality filter with BBDuk, align reads with Hisat2, assemble transcripts with StringTie and Cufflinks,
+and merge the multiple assemblies with Mikado.
+
+
+
 ## Running this example
 
 ### First build the environment

pyrpipe/assembly.py

@@ -59,7 +59,7 @@ def __init__(self,reference_gtf="",**kwargs):
             self.reference_gtf=reference_gtf
             self.passed_args_dict['-G']=reference_gtf
 
-    def perform_assembly(self,bam_file,out_dir="",out_suffix="_stringtie",overwrite=True,verbose=False,quiet=False,logs=True,objectid="NA",**kwargs):
+    def perform_assembly(self,bam_file,out_dir=None,out_suffix="_stringtie",overwrite=True,verbose=False,quiet=False,logs=True,objectid="NA",**kwargs):
         """Function to run stringtie using a bam file.
                 
         Parameters