From 0d4c887ebed4675c8f1b7830d976960651af19fb Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Wed, 20 Nov 2024 14:38:14 +0000
Subject: [PATCH] chore(master): release MPRAsnakeflow 0.4.0

---
 .release-please-manifest.json |  2 +-
 CHANGELOG.md                  | 51 +++++++++++++++++++++++++++++++++++
 version.txt                   |  2 +-
 3 files changed, 53 insertions(+), 2 deletions(-)

diff --git a/.release-please-manifest.json b/.release-please-manifest.json
index 0ee8c01..2537c1f 100644
--- a/.release-please-manifest.json
+++ b/.release-please-manifest.json
@@ -1,3 +1,3 @@
 {
-  ".": "0.3.0"
+  ".": "0.4.0"
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 488f30f..beb8fae 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,56 @@
 # Changelog
 
+## [0.4.0](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.3.0...MPRAsnakeflow-v0.4.0) (2024-11-20)
+
+
+### ⚠ BREAKING CHANGES
+
+* versioned config ([#140](https://github.com/kircherlab/MPRAsnakeflow/issues/140))
+* latest development for new release ([#133](https://github.com/kircherlab/MPRAsnakeflow/issues/133))
+* pseudocounts where not used correctly when RNA or DNA set to 0
+
+### Features
+
+* Add assignment_merge thread configuration ([26e68c2](https://github.com/kircherlab/MPRAsnakeflow/commit/26e68c26f315c524cf28692d636127fbf3bdeb2b))
+* better assignment BC statistics ([00187e6](https://github.com/kircherlab/MPRAsnakeflow/commit/00187e689b2fad10fd317aa2efbd0214fad14434))
+* configurable min mapping quality ([28045ae](https://github.com/kircherlab/MPRAsnakeflow/commit/28045aea23d6fa03f3883b3dc44b3cbc3e8f6205))
+* extending figure width ([8bf81c4](https://github.com/kircherlab/MPRAsnakeflow/commit/8bf81c45e45f9b4c23856c0915bd527f9699b6cd))
+* faster design check ([315b402](https://github.com/kircherlab/MPRAsnakeflow/commit/315b402499d92850382d4110e153602020381e8a))
+* fastq-join implementation ([aaf5315](https://github.com/kircherlab/MPRAsnakeflow/commit/aaf5315364ebb3e3117c3996c2fc357aa9c4d595))
+* latest development for new release ([#133](https://github.com/kircherlab/MPRAsnakeflow/issues/133)) ([bdfc557](https://github.com/kircherlab/MPRAsnakeflow/commit/bdfc557a64cecc19d1d86eead8bdb691a1ff2166))
+* make filtering consistent ([5f7a4c5](https://github.com/kircherlab/MPRAsnakeflow/commit/5f7a4c5a2a3389a75b8d6b7e9aaf34485127b3a4))
+* master variant table ([6bda47c](https://github.com/kircherlab/MPRAsnakeflow/commit/6bda47c78021bc1728bb81a716f5e6daaf6ac084))
+* new final output file with merged replicates ([66cf017](https://github.com/kircherlab/MPRAsnakeflow/commit/66cf0172cb6b556e507be4daabf7e859447787f3))
+* only link assignment fasta when possible ([d7d3822](https://github.com/kircherlab/MPRAsnakeflow/commit/d7d3822933c98d790f3c96bcbfdef1a7ea70c7df)), closes [#50](https://github.com/kircherlab/MPRAsnakeflow/issues/50)
+* remove space, speedup BC extraction ([70e9bd0](https://github.com/kircherlab/MPRAsnakeflow/commit/70e9bd06b91ccb37333e0a69c47917a5eacbf639))
+* replace merging by NGmerge ([0aa8cad](https://github.com/kircherlab/MPRAsnakeflow/commit/0aa8cad6884a953f9c89a2fdd7af397e4e9ccf3e))
+* snakemake 8 compatibility ([cf38ed9](https://github.com/kircherlab/MPRAsnakeflow/commit/cf38ed9de68367d0d1700ccff262e91ad6f1fbc0))
+* snakemake 8 ready with workflow profile ([d637e1f](https://github.com/kircherlab/MPRAsnakeflow/commit/d637e1fdbebfca0616d944101898fbf522df9c82))
+* statistic for assignment workflow ([10c3b26](https://github.com/kircherlab/MPRAsnakeflow/commit/10c3b2677ada59925ddd3de777f7488c9a20e981))
+* using reverese compelment BCs ([d009a6c](https://github.com/kircherlab/MPRAsnakeflow/commit/d009a6c3de7de50a210479b73f5d41969287e234))
+* versioned config ([#140](https://github.com/kircherlab/MPRAsnakeflow/issues/140)) ([9573b66](https://github.com/kircherlab/MPRAsnakeflow/commit/9573b661afb83590b7ac5aedac7b6d3d5e61d8a4))
+
+
+### Bug Fixes
+
+* batch size issue in sort ([487ba8c](https://github.com/kircherlab/MPRAsnakeflow/commit/487ba8ce059517030fcab3708c3cea40ac210f7e))
+* correct use of assignment configs ([58b64f1](https://github.com/kircherlab/MPRAsnakeflow/commit/58b64f1e753477f7410233ac546701ddbd60f9f2))
+* corrected qc_report_assoc ([afb0127](https://github.com/kircherlab/MPRAsnakeflow/commit/afb012750bc1c3c39f2348b283c23ff97695f672))
+* Detach from anaconda ([#122](https://github.com/kircherlab/MPRAsnakeflow/issues/122)) ([16bcea2](https://github.com/kircherlab/MPRAsnakeflow/commit/16bcea2f04190a5965ad1865cf30f6dd44f1b6a0))
+* filter config ([38ee37e](https://github.com/kircherlab/MPRAsnakeflow/commit/38ee37ecfcf4a71b840575504811512e0d64609a))
+* issue with stats and asisgnment ([d935fa1](https://github.com/kircherlab/MPRAsnakeflow/commit/d935fa1f62825dfdcd2cd77e4c73bc37686519a0))
+* memory resources for bbmap ([#123](https://github.com/kircherlab/MPRAsnakeflow/issues/123)) ([af93f58](https://github.com/kircherlab/MPRAsnakeflow/commit/af93f588e9387ddf91197f5587d36c3481499b38))
+* plots per insert only used last experiment. not all. ([c2fd82b](https://github.com/kircherlab/MPRAsnakeflow/commit/c2fd82b6d4b545cc3a1acc5ecb145eb3c93af49d))
+* pseudocounts where not used correctly when RNA or DNA set to 0 ([d2483f9](https://github.com/kircherlab/MPRAsnakeflow/commit/d2483f9c7724e0b63cec4f251519d449831ecf04))
+* remove illegal characters from reference ([0ebee81](https://github.com/kircherlab/MPRAsnakeflow/commit/0ebee81d74f3f6170ce4b8083e18c746550154db))
+* rename barcoe output header ([635f043](https://github.com/kircherlab/MPRAsnakeflow/commit/635f0431c78d3d5bf9b77a16f6ce26d9ff6c82c2))
+* rule make_master_tables fix ([df42845](https://github.com/kircherlab/MPRAsnakeflow/commit/df42845b6dfa9a7b64f187b38f1f15518f3e4a31))
+* statistic total counts ([6381b92](https://github.com/kircherlab/MPRAsnakeflow/commit/6381b928fd6c14eb16801a459b8546fa37004c74))
+* typo in report ([ace8cca](https://github.com/kircherlab/MPRAsnakeflow/commit/ace8ccacb3d7ece04af43c9b0b1dc9c9c087a2c4))
+* upgrade code to new pandas version ([aaea236](https://github.com/kircherlab/MPRAsnakeflow/commit/aaea236bc83f459e7a6c2d3fee96d49c79762325))
+* using correct threads ([6dcad7d](https://github.com/kircherlab/MPRAsnakeflow/commit/6dcad7d34173f37d4538644b1ba0d918afd8f149))
+* using multiple fastq inputs in counts ([95935cf](https://github.com/kircherlab/MPRAsnakeflow/commit/95935cfe69956ca50307a9c6a774c4b96dff860f))
+
 ## [0.3.0](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.2.0...MPRAsnakeflow-v0.3.0) (2024-11-20)
 
 
diff --git a/version.txt b/version.txt
index 0d91a54..1d0ba9e 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-0.3.0
+0.4.0