Commit 74836b3c authored by aknecht2's avatar aknecht2
Browse files

Minor doc fixes.

parent 5443d27d
......@@ -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.
......
......@@ -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
......
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