Bump version: 9.0.1 → 10.0.0

Clinical-Genomics · Jun 27, 2022 · 631c900 · 631c900
1 parent b0cfe6b
commit 631c900
Show file tree

Hide file tree

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 = 9.0.1
+current_version = 10.0.0
 commit = True
 tag = True
 tag_name = v{new_version}
@@ -21,7 +21,6 @@ tag_name = v{new_version}
 [bumpversion:file:docs/install.rst]
 
 [bumpversion:file:docs/balsamic_methods.rst]
-
 search = {current_version}
 replace = {new_version}
 
diff --git a/BALSAMIC/__init__.py b/BALSAMIC/__init__.py
@@ -1 +1 @@
-__version__ = "9.0.1"
+__version__ = "10.0.0"
diff --git a/BALSAMIC/__version__.py b/BALSAMIC/__version__.py
@@ -1 +1 @@
-__version__ = "9.0.1"
+__version__ = "10.0.0"
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="9.0.1"
+LABEL about.version="10.0.0"
 
 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: v9.0.1
+version: v10.0.0
 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/balsamic_logo.png">
         </a>
-        <h3 align="center">Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 9.0.1)</h3>
+        <h3 align="center">Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 10.0.0)</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=v9.0.1 
+.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v10.0.0 
 
 .. |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** = 9.0.1) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 10.0.0) 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 BWA MEM v0.7.17 :superscript:`4`.
@@ -26,7 +26,7 @@ to annotate somatic variants for their population allele frequency from gnomAD v
 Whole Genome Analysis
 ~~~~~~~~~~~~~~~~~~~~~
 
-BALSAMIC :superscript:`1` (**version** = 9.0.1) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 10.0.0) 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 :superscript:`15`.
@@ -46,7 +46,7 @@ to annotate somatic single nucleotide variants for their population allele frequ
 UMI Data Analysis
 ~~~~~~~~~~~~~~~~~~~~~
 
-BALSAMIC :superscript:`1` (**version** = 9.0.1) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 10.0.0) 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`.
 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** = 9.0.1 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each
+BALSAMIC ( **version** = 10.0.0 ) 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.
 
 

diff --git a/docs/install.rst b/docs/install.rst
@@ -2,7 +2,7 @@
 Installation
 ============
 
-This section describes steps to install BALSAMIC (**version** = 9.0.1)
+This section describes steps to install BALSAMIC (**version** = 10.0.0)
 
 
 

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** = 9.0.1).
+Here a short tutorial is provided for BALSAMIC (**version** = 10.0.0).
 
 Running a test sample
 ---------------------