fix star

README.md

@@ -8,11 +8,16 @@
 # pyrpipe: python rna-seq pipeliner
 
 
+
 ## Introduction
 pyrpipe (Pronounced as "pyre-pipe") is a python package to easily develop RNA-Seq analyses workflow by integrating popular RNA-Seq analysis programs in an object oriented manner.
 pyrpipe can be used on local computers or on HPC environments to manage analysis of RNA-Seq data. Users can use the easy-to-use APIs to popular bioinformatic tools provided
 with pyrpipe, or can use the methods provided in the pyrpipe_engine module to integrate any other third-party program in their pipeline.
 
+Preprint is available [here](https://www.biorxiv.org/content/10.1101/2020.03.04.925818v1)
+
+### Note: pyrpipe version 0.0.4 and above is not compatible with lower versions due to changes in the API design.
+
 ### What it does
 Allows fast and easy development of bioinformatics pipelines in python by providing 
 * a high level api to popular bioinformatics tools

case_studies/Maize_lncRNA_prediction/Maize_lncRNAs.ipynb

@@ -276,7 +276,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.5"
+   "version": "3.6.9"
   }
  },
  "nbformat": 4,

pyrpipe/mapping.py

@@ -501,7 +501,7 @@ def perform_alignment(self,sra_object,out_suffix="_star",out_dir="",threads=None
         #determine threads
         if not threads:
             threads=self.threads
-        newOpts["--orunThreadN"]=str(threads)
+        newOpts["--runThreadN"]=str(threads)
 
         #add index
         newOpts["--genomeDir"]=self.star_index

pyrpipe/version.py

@@ -6,4 +6,4 @@
 @author: usingh
 """
 
-__version__="0.0.3"
+__version__="0.0.4"