Merge pull request #140 from cyouh95/DEV_NF_MAAgilent_1ch

- Agilent 1-channel pipeline update from GL-DPPD-7112 to GL-DPPD-7112-A and Workflow update to version 1.0.5
- add support for microarray design annotation that isn't hosted in BioMart
- update software versions and licenses
- refactor pipeline to better document R functions and code

Author: bnovak32

3rd_Party_Licenses/Microarray_Agilent_1_Channel_3rd_Party_Software.md

@@ -1,7 +1,7 @@
 # GeneLab bioinformatics processing pipeline for Agilent 1-channel microarray data
 
 
-> **The document [`GL-DPPD-7112.md`](Pipeline_GL-DPPD-7112_Versions/GL-DPPD-7112.md) holds an overview and example commands for how GeneLab processes Agilent 1-channel microarray datasets. See the [Repository Links](#repository-links) descriptions below for more information. Processed data output files and processing code is provided for each GLDS dataset along with the processed data in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**  
+> **The document [`GL-DPPD-7112-A.md`](Pipeline_GL-DPPD-7112_Versions/GL-DPPD-7112-A.md) holds an overview and example commands for how GeneLab processes Agilent 1-channel microarray datasets. See the [Repository Links](#repository-links) descriptions below for more information. Processed data output files and processing code is provided for each GLDS dataset along with the processed data in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**  
 
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@@ -20,6 +20,7 @@
 
   - Contains instructions for installing and running the GeneLab MAAgilent1ch workflow
 
+
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 **Developed by:**  
 Jonathan Oribello