From aa39f03e4ece5ae3b38f57645e4c21d95f81f8e3 Mon Sep 17 00:00:00 2001
From: urmi-21 <mrbains21@gmail.com>
Date: Mon, 23 Mar 2020 13:18:55 -0500
Subject: [PATCH] fix star

---
 README.md                                                | 5 +++++
 case_studies/Maize_lncRNA_prediction/Maize_lncRNAs.ipynb | 2 +-
 pyrpipe/mapping.py                                       | 2 +-
 pyrpipe/version.py                                       | 2 +-
 4 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 70ac412..ab74059 100644
--- a/README.md
+++ b/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
diff --git a/case_studies/Maize_lncRNA_prediction/Maize_lncRNAs.ipynb b/case_studies/Maize_lncRNA_prediction/Maize_lncRNAs.ipynb
index 74f575d..40eb669 100644
--- a/case_studies/Maize_lncRNA_prediction/Maize_lncRNAs.ipynb
+++ b/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,
diff --git a/pyrpipe/mapping.py b/pyrpipe/mapping.py
index 6bb4048..0b134d8 100644
--- a/pyrpipe/mapping.py
+++ b/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
diff --git a/pyrpipe/version.py b/pyrpipe/version.py
index 045fb45..c0cdb09 100644
--- a/pyrpipe/version.py
+++ b/pyrpipe/version.py
@@ -6,4 +6,4 @@
 @author: usingh
 """
 
-__version__="0.0.3"
\ No newline at end of file
+__version__="0.0.4"
\ No newline at end of file