From 8063eae9fee521ac09f5c5beb1d6bc71fc30edda Mon Sep 17 00:00:00 2001
From: "41898282+github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 13 Jan 2025 20:16:15 +0000
Subject: [PATCH 1/2] =?UTF-8?q?chore:=20=F0=9F=A4=96=20prepare=20release?=
 =?UTF-8?q?=20v0.4.1?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 CHANGELOG.md | 2 +-
 CITATION.cff | 4 ++--
 VERSION      | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9b756c4..a8a886e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,4 @@
-## CHAMPAGNE development version
+## CHAMPAGNE 0.4.1
 
 - The CHAMPAGNE nextflow workflow now has a version entry in `nextflow.config`, in compliance with nf-core. (#213, @kelly-sovacool)
 - Pool input (control) reads of the same sample name by default. Any inputs that should not be pooled must have different sample names in the samplesheet. (#214, @kelly-sovacool)
diff --git a/CITATION.cff b/CITATION.cff
index c5a709a..c835174 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -22,5 +22,5 @@ identifiers:
   - description: Archived snapshots of all versions
     type: doi
     value: 10.5281/zenodo.10516079
-version: v0.4.0
-date-released: "2024-09-11"
+version: v0.4.1
+date-released: "2025-01-13"
diff --git a/VERSION b/VERSION
index 25a5afd..267577d 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.4.0-dev
+0.4.1

From f52c5f019767a92cedfac525fcf33c9b7190e611 Mon Sep 17 00:00:00 2001
From: "41898282+github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 13 Jan 2025 20:18:33 +0000
Subject: [PATCH 2/2] chore: bump changelog & version after release of v0.4.1

---
 CHANGELOG.md | 2 ++
 VERSION      | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a8a886e..629d961 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,5 @@
+## CHAMPAGNE development version
+
 ## CHAMPAGNE 0.4.1
 
 - The CHAMPAGNE nextflow workflow now has a version entry in `nextflow.config`, in compliance with nf-core. (#213, @kelly-sovacool)
diff --git a/VERSION b/VERSION
index 267577d..1351681 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.4.1
+0.4.1-dev