From fd8f3ef177b6a2ec9fc8028e454484844d49a733 Mon Sep 17 00:00:00 2001
From: Mohammed Faizal Eeman Mootor
 <68152431+Faizal-Eeman@users.noreply.github.com>
Date: Thu, 29 Jun 2023 17:06:38 -0700
Subject: [PATCH] Release `docker-Battenberg v2.2.9` (#11)

* add GRCh37 and GRCh38 resources to README

* Update CHANGELOG.md

* fix text indent

* Update README.md based on latest template

* Update README

* Update CHANGELOG.md

---------

Co-authored-by: Mootor <mmootor@ip-0A125250.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>
---
 CHANGELOG.md |  7 ++++---
 README.md    | 32 ++++++++++++++++++++++++++++++++
 2 files changed, 36 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 57144f1..b122cfa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,13 +7,14 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ---
 
-## [Unreleased]
+## [2.2.9] - 2023-06-27
 ### Added
 - Add `modify_reference_path.sh`
+- Add GRCh37 and GRCh38 resource paths to `README.md`
 
 ### Changed
-- Update `README.md`
-- Update Battenberg `v2.2.9`
+- Release `docker-Battenberg v2.2.9`
+- Update Battenberg `v2.2.9` in Dockerfile
 - Reconfigure Dockerfile
 - Standardize Battenberg resource files
 - Standardize the `docker-Battenberg` repo
diff --git a/README.md b/README.md
index 01b5aa6..e6c1c52 100644
--- a/README.md
+++ b/README.md
@@ -3,8 +3,27 @@ This repository contains code for the whole genome sequencing subclonal copy num
 
 It installs the release v2.2.9 of Battenberg and modifies the Battenberg resource paths for GRCh37 and GRCh38 based on how they are structured in the Boutros Lab cluster.
 
+GRCh37 resources - `/hot/ref/tool-specific-input/Battenberg/download_202204/GRCh37/`
+
+GRCh38 resources -
+ - with `chr` name (default): `/hot/ref/tool-specific-input/Battenberg/download_202204/GRCh38/battenberg_ref_hg38_chr/`
+ - without `chr` name: `/hot/ref/tool-specific-input/Battenberg/download_202204/GRCh38/battenberg_ref_hg38_non_chr/`
+
 This image can be found in docker-Battenberg's GitHub package page [here](https://github.com/uclahs-cds/docker-Battenberg/pkgs/container/battenberg).
 
+# Example Usage
+```
+docker run --rm -u $(id -u):$(id -g) -w $(pwd) -v /hot/:/hot/ \
+    -v /hot/ref/tool-specific-input/Battenberg/download_202204/GRCh38/battenberg_ref_hg38_chr/:/opt/battenberg_reference/ \
+    battenberg:2.2.9 Rscript /usr/local/bin/battenberg_wgs.R \
+        -t ${tumor_sample_name} \
+        -n ${normal_sample_name} \
+        --tb ${tumor_bam} \
+        --nb ${normal_bam} \
+        -o ${sample_out_dir} \
+        --sex ${sample_sex}
+```
+
 # Documentation
 Battenberg GitHub repository [here](https://github.com/Wedge-lab/battenberg)
 
@@ -18,6 +37,19 @@ Battenberg GitHub repository [here](https://github.com/Wedge-lab/battenberg)
 |IMPUTE2|2.3.2|
 |ASCAT|3.1.2|
 
+---
+
+## Discussions
+
+- [Issue tracker](https://github.com/uclahs-cds/docker-Battenberg/issues) to report errors and enhancement ideas.
+- Discussions can take place in [docker-Battenberg Discussions](https://github.com/uclahs-cds/docker-Battenberg/discussions)
+- [docker-Battenberg pull requests](https://github.com/uclahs-cds/docker-Battenberg/pulls) are also open for discussion
+
+---
+
+## Contributors
+
+Please see list of [Contributors](https://github.com/uclahs-cds/docker-Battenberg/graphs/contributors) at GitHub.
 
 ---