Minor doc fixes.

chipathlon/workflow.py

@@ -35,11 +35,11 @@ class Workflow(object):
     :type username: str
     :param password: The password to authenticate for MongoDB access.
     :type password: str
-    :param execute_site: A list of sites to submit jobs to.  These sites should
-        be defined in the configuration file.
-    :type execute_site: list
+    :param execute_site: The target site to submit jobs to.  These sites should
+        be defined in the sites.xml file.
+    :type execute_site: str
     :param output_site: The output site to transfer files to.  This site should
-        be defined in the configuration file.
+        be defined in the sites.xml file.
     :type output_site: str
     :param save_db: Whether or not we want to save results to the database.
         True by default.

doc/source/introduction.rst

@@ -10,7 +10,7 @@ steps leading up to and including peak calling can be very computationally
 expensive.  For this reason, we implemented a `Pegasus <pegasus.isi.edu>`_
 pipeline for creating and submitting workflows to super computers.
 
-Currently, there are 7 peak calling tools installed in ChIPathlon:
+Currently, there are 9 peak calling tools installed in ChIPathlon:
 
 1. `Gem <http://groups.csail.mit.edu/cgs/gem/>`_
 2. `Zerone <https://omictools.com/zerone-tool>`_
@@ -19,6 +19,8 @@ Currently, there are 7 peak calling tools installed in ChIPathlon:
 5. `peakranger <http://ranger.sourceforge.net/manual1.18.html>`_
 6. `MUSIC <https://github.com/gersteinlab/MUSIC>`_
 7. `CCAT <https://academic.oup.com/bioinformatics/article/26/9/1199/201375/A-signal-noise-model-for-significance-analysis-of>`_
+8. `PePr <https://github.com/shawnzhangyx/PePr>`_
+9. `hiddenDomains <http://hiddendomains.sourceforge.net/>`_
 
 The pipeline gives the flexibility of choosing any or all of these tools for
 running peak calling, and gives the ability to adjust parameters as necessary