Merge branch 'master' into develop

Author: mathiasbio

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 18.0.0
+current_version = 18.0.1
 commit = True
 tag = True
 tag_name = v{new_version}

BALSAMIC/__init__.py

@@ -1 +1 @@
-__version__ = "18.0.0"
+__version__ = "18.0.1"

BALSAMIC/__version__.py

@@ -1 +1 @@
-__version__ = "18.0.0"
+__version__ = "18.0.1"

CHANGELOG.rst

@@ -1,4 +1,4 @@
-[X.X.X]
+[18.0.1]
 --------
 
 Added:

CITATION.cff

@@ -18,5 +18,5 @@ authors:
 - family-names: "Wirta"
   given-names: "Valtteri"
 title: "BALSAMIC: Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer"
-version: v18.0.0
+version: v18.0.1
 url: "https://github.com/Clinical-Genomics/BALSAMIC"

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 18.0.0)</h3>
+        <h3 align="center">Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 18.0.1)</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=v18.0.0
+.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v18.0.1
 
 .. |snakemake_badge| image:: https://img.shields.io/badge/snakemake-%E2%89%A55.12.3-brightgreen.svg
 

docs/balsamic_methods.rst

@@ -5,7 +5,7 @@ Method description
 Target Genome Analysis
 ~~~~~~~~~~~~~~~~~~~~~~
 
-BALSAMIC :superscript:`1` (**version** = 18.0.0) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 18.0.1) 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** = 18.0.0) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 18.0.1) 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** = 18.0.0) was used to analyze the data from raw FASTQ files.
+BALSAMIC :superscript:`1` (**version** = 18.0.1) 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`.

docs/bioinfo_softwares.rst

@@ -2,7 +2,7 @@
 Tools and software
 =================================
 
-BALSAMIC ( **version** = 18.0.0 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each
+BALSAMIC ( **version** = 18.0.1 ) 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

docs/install.rst

@@ -2,7 +2,7 @@
 Installation
 ============
 
-This section describes steps to install BALSAMIC (**version** = 18.0.0)
+This section describes steps to install BALSAMIC (**version** = 18.0.1)
 
 
 

docs/user_guide.rst

@@ -2,7 +2,7 @@
 Short tutorial
 ==============
 
-Here a short tutorial is provided for BALSAMIC (**version** = 18.0.0).
+Here a short tutorial is provided for BALSAMIC (**version** = 18.0.1).
 
 Regarding fastq-inputs
 ---------------------------