Update docs

CHANGELOG.md

 # v0.0.4 (in development)
 **User Facing**
-* 
+* Add option to pull references from datahub
 
 **Background**
-* 
+* Remove (comment out) option to pull references from S3
+* Make pull references from BioHPC default (including in biohpc.config)
 
 *Known Bugs*
+* Datahub reference pull uses dev.gudmap.org as source until referencencs are placed on production
 * outputBag does not contain fetch for processed data
 * Does not include automatic data upload
 * Override params (inputBag, fastq, species) aren't checked for integrity

README.md

@@ -49,6 +49,9 @@ To Run:
     * *current mouse* **38.p6.vM22** = GRCm38.p6 with GENCODE annotation release M22
     * *current human* **38.p6.v31** = GRCh38.p12 with GENCODE annotation release 31
 * ***Optional*** input overrides
+  * `--refSource` source for pulling references
+    * **biohpc** = source references from BICF_Core gudmap reference local location (workflow must be run on BioHPC system)
+    * **datahub** = source references from GUDMAP/RBK reference_table location (currently uses dev.gudmap.org)
   * `--inputBagForce` utilizes a local replicate inputBag instead of downloading from the data-hub (still requires accurate repRID input)
     * eg: `--inputBagForce test_data/bag/Replicate_Q-Y5F6.zip` (must be the expected bag structure)
   * `--fastqsForce` utilizes local fastq's instead of downloading from the data-hub (still requires accurate repRID input)