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docs: update balsamic method version in bumpversion #930

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merged 3 commits into from May 16, 2022
Merged

docs: update balsamic method version in bumpversion #930

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2881df3
edit version in balsamic methods
May 16, 2022
29df025
update bumpeversion list for version changes
May 16, 2022
5fcd1f3
change log update
May 16, 2022
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3 changes: 3 additions & 0 deletions .bumpversion.cfg
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Expand Up @@ -19,6 +19,9 @@ tag_name = v{new_version}
[bumpversion:file:docs/user_guide.rst]

[bumpversion:file:docs/install.rst]

[bumpversion:file:docs/balsamic_methods.rst]

search = {current_version}
replace = {new_version}

1 change: 1 addition & 0 deletions CHANGELOG.rst
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Expand Up @@ -4,6 +4,7 @@
Fixed:
^^^^^^
* Revert `csvkit` tool in align_qc container #928
* Automatic version update for balsamic methods #930

[9.0.0]
--------
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6 changes: 3 additions & 3 deletions docs/balsamic_methods.rst
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Expand Up @@ -5,7 +5,7 @@ BALSAMIC METHODS
Target Genome Analysis
~~~~~~~~~~~~~~~~~~~~~~

BALSAMIC :superscript:`1` (**version** = 8.2.10) was used to analyze the data from raw FASTQ files.
BALSAMIC :superscript:`1` (**version** = 9.0.1) 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 BWA MEM v0.7.17 :superscript:`4`.
Expand All @@ -26,7 +26,7 @@ to annotate somatic variants for their population allele frequency from gnomAD v
Whole Genome Analysis
~~~~~~~~~~~~~~~~~~~~~

BALSAMIC :superscript:`1` (**version** = 8.2.10) was used to analyze the data from raw FASTQ files.
BALSAMIC :superscript:`1` (**version** = 9.0.1) 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 :superscript:`15`.
Expand All @@ -46,7 +46,7 @@ to annotate somatic variants for their population allele frequency from gnomAD v
UMI Data Analysis
~~~~~~~~~~~~~~~~~~~~~

BALSAMIC :superscript:`1` (**version** = 8.2.10) was used to analyze the data from raw FASTQ files.
BALSAMIC :superscript:`1` (**version** = 9.0.1) 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`.
UMI tag extraction and consensus generation were performed using Sentieon tools v202010.02 :superscript:`15`.
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