diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..12dc373
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,48 @@
+default_install_hook_types: [pre-commit, commit-msg]
+default_stages: [pre-commit]
+exclude: |
+  (?x)(
+      ^assets/|
+      ^docs/.*.html|
+      ^_extensions/
+   )
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.2.3
+    hooks:
+      - id: check-added-large-files
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-json
+  # spell check
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        # https://github.com/codespell-project/codespell/issues/1498
+  # Python formatting
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+  # R formatting
+  - repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.1.2
+    hooks:
+      - id: style-files
+  # general linting
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.7.1
+    hooks:
+      - id: prettier
+  # enforce commit format
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v2.3.0
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]
+        args: []
+  - repo: https://github.com/citation-file-format/cffconvert
+    rev: 054bda51dbe278b3e86f27c890e3f3ac877d616c
+    hooks:
+      - id: validate-cff
diff --git a/.prettierignore b/.prettierignore
new file mode 100644
index 0000000..f0a6037
--- /dev/null
+++ b/.prettierignore
@@ -0,0 +1,8 @@
+# gitignore
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+*.code-workspace
+assets/*.html
diff --git a/.prettierrc b/.prettierrc
new file mode 100644
index 0000000..81ee40a
--- /dev/null
+++ b/.prettierrc
@@ -0,0 +1,7 @@
+overrides:
+  - files:
+      - "*.md"
+      - "*.cff"
+      - ".prettierrc"
+    options:
+      tabWidth: 2
diff --git a/CITATION.cff b/CITATION.cff
index 9ea2218..b940de0 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -1,21 +1,29 @@
 cff-version: 1.2.0
 message: "If you use CARLISLE, please cite it as below."
 authors:
-- family-names: "Sevilla"
-  given-names: "Samantha"
-  orcid: "https://orcid.org/0000-0002-8734-9875"
-- family-names: "Koparde"
-  given-names: "Vishal"
-  orcid: "https://orcid.org/0000-0001-8978-8495"
-- family-names: "Chou"
-  given-names: "Hsien-chao"
-  orcid: "https://orcid.org/0000-0002-4870-9663"
-- family-names: "Kim"
-  given-names: "Sohyoung"
-- family-names: "Hu"
-  given-names: "Yue"
-- family-names: "Saloura"
-  given-names: "Vassiliki"
+  - family-names: "Sevilla"
+    given-names: "Samantha"
+    orcid: "https://orcid.org/0000-0002-8734-9875"
+    affiliation: Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
+  - family-names: "Koparde"
+    given-names: "Vishal"
+    orcid: "https://orcid.org/0000-0001-8978-8495"
+    affiliation: Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
+  - family-names: "Chou"
+    given-names: "Hsien-chao"
+    orcid: "https://orcid.org/0000-0002-4870-9663"
+  - family-names: "Kim"
+    given-names: "Sohyoung"
+  - family-names: "Hu"
+    given-names: "Yue"
+  - family-names: "Saloura"
+    given-names: "Vassiliki"
 title: "Cut And Run anaLysIS pipeLinE (CARLISLE)"
+url: https://ccbr.github.io/CARLISLE/
+repository-code: https://github.com/CCBR/CARLISLE
+identifiers:
+  - description: Archived snapshots of all versions
+    type: doi
+    value: 10.5281/zenodo.10483876
 version: 2.4.1
-url: "https://github.com/CCBR/CARLISLE"
\ No newline at end of file
+date-released: 2024-01-10
diff --git a/README.md b/README.md
index 70fea14..6b2a25c 100644
--- a/README.md
+++ b/README.md
@@ -2,8 +2,11 @@
 
 <div align="center">
   <img src="resources/img/CUTandRUN_Workflow.jpeg" width="85%" height="85%">
-  
-  [![GitHub releases](https://img.shields.io/github/release/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/releases)  [![GitHub issues](https://img.shields.io/github/issues/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/issues) [![GitHub license](https://img.shields.io/github/license/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/blob/master/LICENSE)  
+
+[![GitHub releases](https://img.shields.io/github/release/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/releases)
+[![GitHub issues](https://img.shields.io/github/issues/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/issues)
+[![GitHub license](https://img.shields.io/github/license/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/blob/master/LICENSE)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10483876.svg)](https://doi.org/10.5281/zenodo.10483876)
 
 </div>