diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 2f03ecc60..493d576fa 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 10.0.2 +current_version = 10.0.3 commit = True tag = True tag_name = v{new_version} diff --git a/BALSAMIC/__init__.py b/BALSAMIC/__init__.py index b7a5e0790..069a364b4 100644 --- a/BALSAMIC/__init__.py +++ b/BALSAMIC/__init__.py @@ -1 +1 @@ -__version__ = "10.0.2" +__version__ = "10.0.3" diff --git a/BALSAMIC/__version__.py b/BALSAMIC/__version__.py index b7a5e0790..069a364b4 100644 --- a/BALSAMIC/__version__.py +++ b/BALSAMIC/__version__.py @@ -1 +1 @@ -__version__ = "10.0.2" +__version__ = "10.0.3" diff --git a/BALSAMIC/containers/balsamic/Dockerfile b/BALSAMIC/containers/balsamic/Dockerfile index 4c82a4ba3..977fa908d 100644 --- 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="10.0.2" +LABEL about.version="10.0.3" ENV PATH="/opt/conda/bin/:${PATH}" ENV MUSL_LOCPATH="/usr/share/i18n/locales/musl" diff --git a/CITATION.cff b/CITATION.cff index 2cedf9ee9..972fbdaa7 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: v10.0.2 +version: v10.0.3 url: "https://github.com/Clinical-Genomics/BALSAMIC" diff --git a/README.rst b/README.rst index d21fc6d8c..f9cf89e27 100644 --- a/README.rst +++ b/README.rst @@ -4,7 +4,7 @@ -

Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 10.0.2)

+

Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 10.0.3)

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=v10.0.2 +.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v10.0.3 .. |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 112954e3c..ea852706d 100644 --- a/docs/balsamic_methods.rst +++ b/docs/balsamic_methods.rst @@ -5,7 +5,7 @@ Method description Target Genome Analysis ~~~~~~~~~~~~~~~~~~~~~~ -BALSAMIC :superscript:`1` (**version** = 10.0.2) was used to analyze the data from raw FASTQ files. +BALSAMIC :superscript:`1` (**version** = 10.0.3) 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** = 10.0.2) was used to analyze the data from raw FASTQ files. +BALSAMIC :superscript:`1` (**version** = 10.0.3) 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** = 10.0.2) was used to analyze the data from raw FASTQ files. +BALSAMIC :superscript:`1` (**version** = 10.0.3) 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 index 620ae3e9e..5f356a8cb 100644 --- a/docs/bioinfo_softwares.rst +++ b/docs/bioinfo_softwares.rst @@ -2,7 +2,7 @@ Tools and software ================================= -BALSAMIC ( **version** = 10.0.2 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each +BALSAMIC ( **version** = 10.0.3 ) 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 index 1581219ef..2bbfc289e 100644 --- a/docs/install.rst +++ b/docs/install.rst @@ -2,7 +2,7 @@ Installation ============ -This section describes steps to install BALSAMIC (**version** = 10.0.2) +This section describes steps to install BALSAMIC (**version** = 10.0.3) diff --git a/docs/user_guide.rst b/docs/user_guide.rst index 696e0d3e6..823584f67 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** = 10.0.2). +Here a short tutorial is provided for BALSAMIC (**version** = 10.0.3). Running a test sample ---------------------