Bump version: 12.0.2 → 13.0.0

Clinical-Genomics · Jan 19, 2024 · ae1788a · ae1788a
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Showing 10 changed files with 13 additions and 14 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 12.0.2
+current_version = 13.0.0
 commit = True
 tag = True
 tag_name = v{new_version}
@@ -21,6 +21,5 @@ tag_name = v{new_version}
 [bumpversion:file:docs/balsamic_methods.rst]
 
 [bumpversion:file:setup.py]
-
 search = {current_version}
 replace = {new_version}
diff --git a/BALSAMIC/__init__.py b/BALSAMIC/__init__.py
@@ -1 +1 @@
-__version__ = "12.0.2"
+__version__ = "13.0.0"
diff --git a/BALSAMIC/__version__.py b/BALSAMIC/__version__.py
@@ -1 +1 @@
-__version__ = "12.0.2"
+__version__ = "13.0.0"
diff --git 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: v12.0.2
+version: v13.0.0
 url: "https://github.com/Clinical-Genomics/BALSAMIC"
diff --git a/README.rst b/README.rst
@@ -4,7 +4,7 @@
         <a href="https://github.com/Clinical-Genomics/BALSAMIC">
             <img  width=480 src="https://raw.githubusercontent.com/Clinical-Genomics/BALSAMIC/master/BALSAMIC/assets/images/balsamic_logo.png">
         </a>
-        <h3 align="center">Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 12.0.2)</h3>
+        <h3 align="center">Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 13.0.0)</h3>
         <h3 align="center">FastQ to Annotated VCF</h3>
     </p>
 
@@ -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=v12.0.2
+.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v13.0.0
 
 .. |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
@@ -5,7 +5,7 @@ Method description
 Target Genome Analysis
 ~~~~~~~~~~~~~~~~~~~~~~
 
-BALSAMIC :superscript:`1` (**version** = 12.0.2) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 13.0.0) 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 202010.02 :superscript:`15`.
@@ -26,7 +26,7 @@ to annotate somatic variants for their population allele frequency from gnomAD v
 Whole Genome Analysis
 ~~~~~~~~~~~~~~~~~~~~~
 
-BALSAMIC :superscript:`1` (**version** = 12.0.2) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 13.0.0) 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 202010.02 :superscript:`15`.
@@ -46,7 +46,7 @@ to annotate somatic single nucleotide variants for their population allele frequ
 UMI Data Analysis
 ~~~~~~~~~~~~~~~~~~~~~
 
-BALSAMIC :superscript:`1` (**version** = 12.0.2) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 13.0.0) was used to analyze the data from raw FASTQ files.
 We first quality controlled FASTQ files using FastQC v0.11.9 :superscript:`2`.
 UMI tag extraction and consensus generation were performed using Sentieon tools v202010.02 :superscript:`15`.
 Adapter sequences and low-quality bases were trimmed using fastp v0.23.2 :superscript:`3`.

diff --git a/docs/bioinfo_softwares.rst b/docs/bioinfo_softwares.rst
@@ -2,7 +2,7 @@
 Tools and software
 =================================
 
-BALSAMIC ( **version** = 12.0.2 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each
+BALSAMIC ( **version** = 13.0.0 ) 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
@@ -2,7 +2,7 @@
 Installation
 ============
 
-This section describes steps to install BALSAMIC (**version** = 12.0.2)
+This section describes steps to install BALSAMIC (**version** = 13.0.0)
 
 
 

diff --git 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** = 12.0.2).
+Here a short tutorial is provided for BALSAMIC (**version** = 13.0.0).
 
 Regarding fastq-inputs
 ---------------------

diff --git a/setup.py b/setup.py
@@ -122,7 +122,7 @@
 
 setup(
     name=NAME,
-    version="12.0.2",
+    version="13.0.0",
     url=URL,
     author=AUTHOR,
     author_email=EMAIL,