From c8a7ab57eea80e7a8443c669fa84d6eb7df334df Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 14 Sep 2020 09:33:45 -0500
Subject: [PATCH] Update docs
---
CHANGELOG.md | 6 ++++--
README.md | 3 +++
2 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e4072e3..496ad67 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,11 +1,13 @@
# 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
diff --git a/README.md b/README.md
index 49069c5..e3134bf 100644
--- a/README.md
+++ b/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)
--
GitLab