From ae1788a67eb1ba351a195b579e0ee17874611052 Mon Sep 17 00:00:00 2001 From: Mathias Johansson Date: Fri, 19 Jan 2024 16:30:12 +0100 Subject: [PATCH] =?UTF-8?q?Bump=20version:=2012.0.2=20=E2=86=92=2013.0.0?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 3 +-- BALSAMIC/__init__.py | 2 +- BALSAMIC/__version__.py | 2 +- CITATION.cff | 2 +- README.rst | 4 ++-- docs/balsamic_methods.rst | 6 +++--- docs/bioinfo_softwares.rst | 2 +- docs/install.rst | 2 +- docs/user_guide.rst | 2 +- setup.py | 2 +- 10 files changed, 13 insertions(+), 14 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 981991c01..d5185f403 100644 --- 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 index 147085852..1311252a5 100644 --- 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 index 147085852..1311252a5 100644 --- 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 index 089ff5224..6f811a1a1 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: v12.0.2 +version: v13.0.0 url: "https://github.com/Clinical-Genomics/BALSAMIC" diff --git a/README.rst b/README.rst index ee78c9bb7..e1bc99897 100644 --- a/README.rst +++ b/README.rst @@ -4,7 +4,7 @@ -

Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 12.0.2)

+

Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 13.0.0)

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=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 index ad18ffc4c..372e69287 100644 --- 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 index f6dcf34cf..138abf4f7 100644 --- 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 index f6d65fa52..11bdd5e4c 100644 --- 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 index 1b20d8e8e..ff28fde3c 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** = 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 index 43d355725..8dab0e62d 100644 --- 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,