Bump version: 11.1.0 → 11.2.0

Clinical-Genomics · Feb 14, 2023 · 36a66e8 · 36a66e8
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 11.1.0
+current_version = 11.2.0
 commit = True
 tag = True
 tag_name = v{new_version}

diff --git a/BALSAMIC/__init__.py b/BALSAMIC/__init__.py
@@ -1 +1 @@
-__version__ = "11.1.0"
+__version__ = "11.2.0"
diff --git a/BALSAMIC/__version__.py b/BALSAMIC/__version__.py
@@ -1 +1 @@
-__version__ = "11.1.0"
+__version__ = "11.2.0"
diff --git a/BALSAMIC/containers/balsamic/Dockerfile b/BALSAMIC/containers/balsamic/Dockerfile
@@ -6,7 +6,7 @@ LABEL about.documentation="https://balsamic.readthedocs.io/"
 LABEL about.license="MIT License (MIT)"
 LABEL about.maintainer="Hassan Foroughi hassan dot foroughi at scilifelab dot se" 
 LABEL about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
-LABEL about.version="11.1.0"
+LABEL about.version="11.2.0"
 
 ENV PATH="/opt/conda/bin/:${PATH}"
 ENV MUSL_LOCPATH="/usr/share/i18n/locales/musl"

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: v11.1.0
+version: v11.2.0
 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/balsamic_logo.png">
         </a>
-        <h3 align="center">Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 11.1.0)</h3>
+        <h3 align="center">Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 11.2.0)</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=v11.1.0 
+.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v11.2.0 
 
 .. |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** = 11.1.0) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 11.2.0) 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 BWA MEM v0.7.17 :superscript:`4`.
@@ -27,7 +27,7 @@ to annotate somatic variants for their population allele frequency from gnomAD v
 Whole Genome Analysis
 ~~~~~~~~~~~~~~~~~~~~~
 
-BALSAMIC :superscript:`1` (**version** = 11.1.0) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 11.2.0) 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 :superscript:`15`.
@@ -47,7 +47,7 @@ to annotate somatic single nucleotide variants for their population allele frequ
 UMI Data Analysis
 ~~~~~~~~~~~~~~~~~~~~~
 
-BALSAMIC :superscript:`1` (**version** = 11.1.0) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 11.2.0) 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`.
 UMI tag extraction and consensus generation were performed using Sentieon tools v202010.02 :superscript:`15`.

diff --git a/docs/bioinfo_softwares.rst b/docs/bioinfo_softwares.rst
@@ -2,7 +2,7 @@
 Tools and software
 =================================
 
-BALSAMIC ( **version** = 11.1.0 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each
+BALSAMIC ( **version** = 11.2.0 ) 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.
 
 

diff --git a/docs/install.rst b/docs/install.rst
@@ -2,7 +2,7 @@
 Installation
 ============
 
-This section describes steps to install BALSAMIC (**version** = 11.1.0)
+This section describes steps to install BALSAMIC (**version** = 11.2.0)
 
 
 

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** = 11.1.0).
+Here a short tutorial is provided for BALSAMIC (**version** = 11.2.0).
 
 Running a test sample
 ---------------------