From b9c59a4a0beacc11a75a502ef46a7db353aa982b Mon Sep 17 00:00:00 2001 From: Eva Caceres Date: Tue, 7 Feb 2023 14:24:13 +0100 Subject: [PATCH] =?UTF-8?q?Bump=20version:=2011.0.2=20=E2=86=92=2011.1.0?= 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 +- BALSAMIC/containers/balsamic/Dockerfile | 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 +- 10 files changed, 13 insertions(+), 13 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index fb0424e79..bdf217011 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 11.0.2 +current_version = 11.1.0 commit = True tag = True tag_name = v{new_version} diff --git a/BALSAMIC/__init__.py b/BALSAMIC/__init__.py index 41238981b..f9e29a7cd 100644 --- a/BALSAMIC/__init__.py +++ b/BALSAMIC/__init__.py @@ -1 +1 @@ -__version__ = "11.0.2" +__version__ = "11.1.0" diff --git a/BALSAMIC/__version__.py b/BALSAMIC/__version__.py index 41238981b..f9e29a7cd 100644 --- a/BALSAMIC/__version__.py +++ b/BALSAMIC/__version__.py @@ -1 +1 @@ -__version__ = "11.0.2" +__version__ = "11.1.0" diff --git a/BALSAMIC/containers/balsamic/Dockerfile b/BALSAMIC/containers/balsamic/Dockerfile index 15409a67e..af1489a77 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="11.0.2" +LABEL about.version="11.1.0" ENV PATH="/opt/conda/bin/:${PATH}" ENV MUSL_LOCPATH="/usr/share/i18n/locales/musl" diff --git a/CITATION.cff b/CITATION.cff index caf86ee40..0f2d1e467 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: v11.0.2 +version: v11.1.0 url: "https://github.com/Clinical-Genomics/BALSAMIC" diff --git a/README.rst b/README.rst index 66e2340d9..e32b903dc 100644 --- a/README.rst +++ b/README.rst @@ -4,7 +4,7 @@ -

Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 11.0.2)

+

Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 11.1.0)

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=v11.0.2 +.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v11.1.0 .. |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 79f79dafd..4d2c1a13f 100644 --- a/docs/balsamic_methods.rst +++ b/docs/balsamic_methods.rst @@ -5,7 +5,7 @@ Method description Target Genome Analysis ~~~~~~~~~~~~~~~~~~~~~~ -BALSAMIC :superscript:`1` (**version** = 11.0.2) was used to analyze the data from raw FASTQ files. +BALSAMIC :superscript:`1` (**version** = 11.1.0) 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`. @@ -27,7 +27,7 @@ to annotate somatic variants for their population allele frequency from gnomAD v Whole Genome Analysis ~~~~~~~~~~~~~~~~~~~~~ -BALSAMIC :superscript:`1` (**version** = 11.0.2) was used to analyze the data from raw FASTQ files. +BALSAMIC :superscript:`1` (**version** = 11.1.0) 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`. @@ -47,7 +47,7 @@ to annotate somatic single nucleotide variants for their population allele frequ UMI Data Analysis ~~~~~~~~~~~~~~~~~~~~~ -BALSAMIC :superscript:`1` (**version** = 11.0.2) was used to analyze the data from raw FASTQ files. +BALSAMIC :superscript:`1` (**version** = 11.1.0) 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 index 52492a2f3..276ce80ee 100644 --- a/docs/bioinfo_softwares.rst +++ b/docs/bioinfo_softwares.rst @@ -2,7 +2,7 @@ Tools and software ================================= -BALSAMIC ( **version** = 11.0.2 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each +BALSAMIC ( **version** = 11.1.0 ) 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 index a763f7a20..dee5148c2 100644 --- a/docs/install.rst +++ b/docs/install.rst @@ -2,7 +2,7 @@ Installation ============ -This section describes steps to install BALSAMIC (**version** = 11.0.2) +This section describes steps to install BALSAMIC (**version** = 11.1.0) diff --git a/docs/user_guide.rst b/docs/user_guide.rst index 7f2200a07..7c3baba0d 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** = 11.0.2). +Here a short tutorial is provided for BALSAMIC (**version** = 11.1.0). Running a test sample ---------------------