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feat: Bumpversion #1504

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feat: Bumpversion #1504

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5293e36
changelog
khurrammaqbool Nov 19, 2024
4b3959d
Bump version: 15.0.1 → 16.0.0
khurrammaqbool Nov 19, 2024
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2 changes: 1 addition & 1 deletion .bumpversion.cfg
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@@ -1,5 +1,5 @@
[bumpversion]
current_version = 15.0.1
current_version = 16.0.0
commit = True
tag = True
tag_name = v{new_version}
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2 changes: 1 addition & 1 deletion BALSAMIC/__init__.py
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__version__ = "15.0.1"
__version__ = "16.0.0"
2 changes: 1 addition & 1 deletion BALSAMIC/__version__.py
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__version__ = "15.0.1"
__version__ = "16.0.0"
1 change: 0 additions & 1 deletion CHANGELOG.rst
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Expand Up @@ -40,7 +40,6 @@ Changed:
* Updated readthedocs tools versions https://github.com/Clinical-Genomics/BALSAMIC/pull/1489
* Renamed UMI consensusfiltered bamfile to be picked up by multiqc https://github.com/Clinical-Genomics/BALSAMIC/pull/1490


Removed:
^^^^^^^^
* GATK3 https://github.com/Clinical-Genomics/BALSAMIC/pull/1432
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2 changes: 1 addition & 1 deletion CITATION.cff
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Expand Up @@ -18,5 +18,5 @@ authors:
- family-names: "Wirta"
given-names: "Valtteri"
title: "BALSAMIC: Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer"
version: v15.0.1
version: v16.0.0
url: "https://github.com/Clinical-Genomics/BALSAMIC"
4 changes: 2 additions & 2 deletions README.rst
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Expand Up @@ -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 15.0.1)</h3>
<h3 align="center">Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 16.0.0)</h3>
<h3 align="center">FastQ to Annotated VCF</h3>
</p>

Expand Down Expand Up @@ -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=v15.0.1
.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v16.0.0

.. |snakemake_badge| image:: https://img.shields.io/badge/snakemake-%E2%89%A55.12.3-brightgreen.svg

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6 changes: 3 additions & 3 deletions docs/balsamic_methods.rst
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Expand Up @@ -5,7 +5,7 @@ Method description
Target Genome Analysis
~~~~~~~~~~~~~~~~~~~~~~

BALSAMIC :superscript:`1` (**version** = 15.0.1) was used to analyze the data from raw FASTQ files.
BALSAMIC :superscript:`1` (**version** = 16.0.0) 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 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`.
Expand All @@ -25,7 +25,7 @@ to annotate somatic variants for their population allele frequency from gnomAD v
Whole Genome Analysis
~~~~~~~~~~~~~~~~~~~~~

BALSAMIC :superscript:`1` (**version** = 15.0.1) was used to analyze the data from raw FASTQ files.
BALSAMIC :superscript:`1` (**version** = 16.0.0) 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 202308.03 :superscript:`15`.
Expand All @@ -45,7 +45,7 @@ to annotate somatic single nucleotide variants for their population allele frequ
UMI workflow
~~~~~~~~~~~~~~~~~~~~~

BALSAMIC :superscript:`1` (**version** = 15.0.1) was used to analyze the data from raw FASTQ files.
BALSAMIC :superscript:`1` (**version** = 16.0.0) 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 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`.
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2 changes: 1 addition & 1 deletion docs/bioinfo_softwares.rst
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Expand Up @@ -2,7 +2,7 @@
Tools and software
=================================

BALSAMIC ( **version** = 15.0.1 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each
BALSAMIC ( **version** = 16.0.0 ) 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
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2 changes: 1 addition & 1 deletion docs/install.rst
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Installation
============

This section describes steps to install BALSAMIC (**version** = 15.0.1)
This section describes steps to install BALSAMIC (**version** = 16.0.0)



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2 changes: 1 addition & 1 deletion docs/user_guide.rst
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Expand Up @@ -2,10 +2,10 @@
Short tutorial
==============

Here a short tutorial is provided for BALSAMIC (**version** = 15.0.1).
Here a short tutorial is provided for BALSAMIC (**version** = 16.0.0).

Regarding fastq-inputs
---------------------

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GitHub Actions / docs 

Title underline too short.

Previous versions of BALSAMIC only accepted one fastq-pair per sample, which required concatenation of fastq-pairs if multiple existed.

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4 changes: 2 additions & 2 deletions setup.py
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Expand Up @@ -25,7 +25,7 @@
"charset-normalizer==3.2.0",
"click==8.1.6",
"colorclass==2.2.2",
"coloredlogs==15.0.1",
"coloredlogs==16.0.0",
"ConfigArgParse==1.7",
"connection-pool==0.0.3",
"contourpy==1.1.0",
Expand Down Expand Up @@ -122,7 +122,7 @@

setup(
name=NAME,
version="15.0.1",
version="16.0.0",
url=URL,
author=AUTHOR,
author_email=EMAIL,
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