diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 8903147b2..79aabbb5a 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
[bumpversion]
-current_version = 15.0.1
+current_version = 16.0.0
commit = True
tag = True
tag_name = v{new_version}
diff --git a/BALSAMIC/__init__.py b/BALSAMIC/__init__.py
index e84bc9e25..5e5e9109a 100644
--- a/BALSAMIC/__init__.py
+++ b/BALSAMIC/__init__.py
@@ -1 +1 @@
-__version__ = "15.0.1"
+__version__ = "16.0.0"
diff --git a/BALSAMIC/__version__.py b/BALSAMIC/__version__.py
index e84bc9e25..5e5e9109a 100644
--- a/BALSAMIC/__version__.py
+++ b/BALSAMIC/__version__.py
@@ -1 +1 @@
-__version__ = "15.0.1"
+__version__ = "16.0.0"
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index a79aa97fd..15ae88b97 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -40,7 +40,6 @@ Changed:
* Updated readthedocs tools versions https://github.com/Clinical-Genomics/BALSAMIC/pull/1489
* Renamed UMI consensusfiltered bamfile to be picked up by multiqc https://github.com/Clinical-Genomics/BALSAMIC/pull/1490
-
Removed:
^^^^^^^^
* GATK3 https://github.com/Clinical-Genomics/BALSAMIC/pull/1432
diff --git a/CITATION.cff b/CITATION.cff
index 70042a152..4fbcedbfd 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -18,5 +18,5 @@ authors:
- family-names: "Wirta"
given-names: "Valtteri"
title: "BALSAMIC: Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer"
-version: v15.0.1
+version: v16.0.0
url: "https://github.com/Clinical-Genomics/BALSAMIC"
diff --git a/README.rst b/README.rst
index e4caf4fad..366716c91 100644
--- a/README.rst
+++ b/README.rst
@@ -4,7 +4,7 @@
- Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 15.0.1)
+ Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 16.0.0)
FastQ to Annotated VCF
@@ -56,7 +56,7 @@ Snakemake cli given that there is a proper config file created.
.. |docker_latest_build_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push.yml/badge.svg
-.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v15.0.1
+.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v16.0.0
.. |snakemake_badge| image:: https://img.shields.io/badge/snakemake-%E2%89%A55.12.3-brightgreen.svg
diff --git a/docs/balsamic_methods.rst b/docs/balsamic_methods.rst
index d4b206208..01fe39dff 100644
--- a/docs/balsamic_methods.rst
+++ b/docs/balsamic_methods.rst
@@ -5,7 +5,7 @@ Method description
Target Genome Analysis
~~~~~~~~~~~~~~~~~~~~~~
-BALSAMIC :superscript:`1` (**version** = 15.0.1) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 16.0.0) was used to analyze the data from raw FASTQ files.
We first quality controlled FASTQ files using FastQC v0.11.9 :superscript:`2`.
Adapter sequences are trimmed using fastp v0.23.2 :superscript:`3` and then UMI sequences are extracted using the UMI extract tool from sentieon-tools (version 202308.03) :superscript:`15` and finally low-quality bases were trimmed using fastp v0.23.2 :superscript:`3`.
Trimmed reads were mapped to the reference genome hg19 using sentieon-tools :superscript:`15`.
@@ -25,7 +25,7 @@ to annotate somatic variants for their population allele frequency from gnomAD v
Whole Genome Analysis
~~~~~~~~~~~~~~~~~~~~~
-BALSAMIC :superscript:`1` (**version** = 15.0.1) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 16.0.0) was used to analyze the data from raw FASTQ files.
We first quality controlled FASTQ files using FastQC v0.11.9 :superscript:`2`.
Adapter sequences and low-quality bases were trimmed using fastp v0.23.2 :superscript:`3`.
Trimmed reads were mapped to the reference genome hg19 using sentieon-tools 202308.03 :superscript:`15`.
@@ -45,7 +45,7 @@ to annotate somatic single nucleotide variants for their population allele frequ
UMI workflow
~~~~~~~~~~~~~~~~~~~~~
-BALSAMIC :superscript:`1` (**version** = 15.0.1) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 16.0.0) was used to analyze the data from raw FASTQ files.
We first quality controlled FASTQ files using FastQC v0.11.9 :superscript:`2`.
Adapter sequences were trimmed using fastp v0.23.2 :superscript:`3`.
UMI tag extraction and alignment and consensus-calling of UMI groups were performed using Sentieon tools 202308.03 :superscript:`15`.
diff --git a/docs/bioinfo_softwares.rst b/docs/bioinfo_softwares.rst
index 8f1a2f94a..72af0b844 100644
--- a/docs/bioinfo_softwares.rst
+++ b/docs/bioinfo_softwares.rst
@@ -2,7 +2,7 @@
Tools and software
=================================
-BALSAMIC ( **version** = 15.0.1 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each
+BALSAMIC ( **version** = 16.0.0 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each
one is included: usage and parameters, and relevant external links.
ascatNgs
diff --git a/docs/install.rst b/docs/install.rst
index 89634021a..ce0517f11 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -2,7 +2,7 @@
Installation
============
-This section describes steps to install BALSAMIC (**version** = 15.0.1)
+This section describes steps to install BALSAMIC (**version** = 16.0.0)
diff --git a/docs/user_guide.rst b/docs/user_guide.rst
index fab7cb134..00db4bf9d 100644
--- a/docs/user_guide.rst
+++ b/docs/user_guide.rst
@@ -2,7 +2,7 @@
Short tutorial
==============
-Here a short tutorial is provided for BALSAMIC (**version** = 15.0.1).
+Here a short tutorial is provided for BALSAMIC (**version** = 16.0.0).
Regarding fastq-inputs
---------------------
diff --git a/setup.py b/setup.py
index a76e9735d..855488948 100644
--- a/setup.py
+++ b/setup.py
@@ -25,7 +25,7 @@
"charset-normalizer==3.2.0",
"click==8.1.6",
"colorclass==2.2.2",
- "coloredlogs==15.0.1",
+ "coloredlogs==16.0.0",
"ConfigArgParse==1.7",
"connection-pool==0.0.3",
"contourpy==1.1.0",
@@ -122,7 +122,7 @@
setup(
name=NAME,
- version="15.0.1",
+ version="16.0.0",
url=URL,
author=AUTHOR,
author_email=EMAIL,