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chore: update doc tool versions #1489

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merged 9 commits into from
Oct 17, 2024
Merged

chore: update doc tool versions #1489

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fedcb8f
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Oct 17, 2024
2007528
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Oct 17, 2024
3fb6de2
Merge branch 'develop' into update_doc_tool_versions
mathiasbio Oct 17, 2024
17b806e
update tool versions
mathiasbio Oct 17, 2024
354c31d
changelog
mathiasbio Oct 17, 2024
ce94f8d
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Oct 17, 2024
d4366af
change bcftools version
mathiasbio Oct 17, 2024
7c72dde
solve merge conflict
mathiasbio Oct 17, 2024
6f0838e
remove DS store
mathiasbio Oct 17, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.rst
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Expand Up @@ -36,8 +36,10 @@ Changed:
* Lowered maximal SOR for TNscope in TGA tumor only cases from 3 to 2.7 https://github.com/Clinical-Genomics/BALSAMIC/pull/1475
* Fixed TNscope research VCF filters to either PASS or triallelic site https://github.com/Clinical-Genomics/BALSAMIC/pull/1475
* Increased maximal amount of redirects for lychee test following links in docs to 10 https://github.com/Clinical-Genomics/BALSAMIC/pull/1488
* 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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8 changes: 4 additions & 4 deletions docs/bioinfo_softwares.rst
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Expand Up @@ -15,7 +15,7 @@ bcftools
~~~~~~~~
:Source code: `GitHub` `<https://github.com/samtools/bcftools>`_
:Article: `Bioinformatics` `<https://pubmed.ncbi.nlm.nih.gov/21903627/>`_
:Version: `>=1.10`
:Version: `>=1.13`

bedtools
~~~~~~~~
Expand Down Expand Up @@ -74,7 +74,7 @@ fastqc
genmod
~~~~~~
:Source code: `Github` `<https://github.com/Clinical-Genomics/genmod>`_
:Version: `0.2.16`
:Version: `3.7.4`

manta
~~~~~
Expand Down Expand Up @@ -116,7 +116,7 @@ samtools
~~~~~~~~
:Source code: `GitHub` `<https://github.com/samtools/samtools>`_
:Article: `Bioinformatics` `<https://pubmed.ncbi.nlm.nih.gov/19505943/>`_
:Version: `>1.11`
:Version: `1.15.1`

sentieon-tools
~~~~~~~~~~~~~~
Expand Down Expand Up @@ -164,4 +164,4 @@ vcf2cytosure
~~~~~~~~~~~~~
:Source code: `GitHub` `<https://github.com/NBISweden/vcf2cytosure>`_
:Article: `-`
:Version: `0.8`
:Version: `0.9.1`
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