From bac844057beb341eebdf88260fb36e59999faa61 Mon Sep 17 00:00:00 2001 From: Mathias Johansson Date: Mon, 10 Feb 2025 15:39:31 +0100 Subject: [PATCH] =?UTF-8?q?Bump=20version:=2016.0.0=20=E2=86=92=2016.0.1?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- 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(+), 13 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 79aabbb5a..699ac60ba 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 16.0.0 +current_version = 16.0.1 commit = True tag = True tag_name = v{new_version} diff --git a/BALSAMIC/__init__.py b/BALSAMIC/__init__.py index 5e5e9109a..610c11155 100644 --- a/BALSAMIC/__init__.py +++ b/BALSAMIC/__init__.py @@ -1 +1 @@ -__version__ = "16.0.0" +__version__ = "16.0.1" diff --git a/BALSAMIC/__version__.py b/BALSAMIC/__version__.py index 5e5e9109a..610c11155 100644 --- a/BALSAMIC/__version__.py +++ b/BALSAMIC/__version__.py @@ -1 +1 @@ -__version__ = "16.0.0" +__version__ = "16.0.1" diff --git a/CITATION.cff b/CITATION.cff index 4fbcedbfd..3f536e96c 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: v16.0.0 +version: v16.0.1 url: "https://github.com/Clinical-Genomics/BALSAMIC" diff --git a/README.rst b/README.rst index 366716c91..19969658c 100644 --- a/README.rst +++ b/README.rst @@ -4,7 +4,7 @@ -

Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 16.0.0)

+

Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 16.0.1)

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=v16.0.0 +.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v16.0.1 .. |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 01fe39dff..bb25ee7d1 100644 --- a/docs/balsamic_methods.rst +++ b/docs/balsamic_methods.rst @@ -5,7 +5,7 @@ Method description Target Genome Analysis ~~~~~~~~~~~~~~~~~~~~~~ -BALSAMIC :superscript:`1` (**version** = 16.0.0) was used to analyze the data from raw FASTQ files. +BALSAMIC :superscript:`1` (**version** = 16.0.1) 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** = 16.0.0) was used to analyze the data from raw FASTQ files. +BALSAMIC :superscript:`1` (**version** = 16.0.1) 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** = 16.0.0) was used to analyze the data from raw FASTQ files. +BALSAMIC :superscript:`1` (**version** = 16.0.1) 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`. diff --git a/docs/bioinfo_softwares.rst b/docs/bioinfo_softwares.rst index 72af0b844..d871989a1 100644 --- a/docs/bioinfo_softwares.rst +++ b/docs/bioinfo_softwares.rst @@ -2,7 +2,7 @@ Tools and software ================================= -BALSAMIC ( **version** = 16.0.0 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each +BALSAMIC ( **version** = 16.0.1 ) 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 diff --git a/docs/install.rst b/docs/install.rst index ce0517f11..6b4efbffd 100644 --- a/docs/install.rst +++ b/docs/install.rst @@ -2,7 +2,7 @@ Installation ============ -This section describes steps to install BALSAMIC (**version** = 16.0.0) +This section describes steps to install BALSAMIC (**version** = 16.0.1) diff --git a/docs/user_guide.rst b/docs/user_guide.rst index 00db4bf9d..3b6459b6d 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** = 16.0.0). +Here a short tutorial is provided for BALSAMIC (**version** = 16.0.1). Regarding fastq-inputs --------------------- diff --git a/setup.py b/setup.py index 00bd3b1c5..a057c3c13 100644 --- a/setup.py +++ b/setup.py @@ -122,7 +122,7 @@ setup( name=NAME, - version="16.0.0", + version="16.0.1", url=URL, author=AUTHOR, author_email=EMAIL,