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fix: update MSI table #1459

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Jun 28, 2024
Merged

fix: update MSI table #1459

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3cec71e
update MSI table
khurrammaqbool Jun 28, 2024
19bfe34
changelog
khurrammaqbool Jun 28, 2024
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2 changes: 1 addition & 1 deletion BALSAMIC/snakemake_rules/annotation/msi_tumor_normal.rule
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Expand Up @@ -47,7 +47,7 @@ rule msisensorpro_msi_tumor_normal:
"""
msisensor-pro msi -b {threads} -z 1 -d {input.msi_list} -t {input.bamT} -n {input.bamN} -o {params.tmpdir}/msi_{params.case_id};

cp {params.tmpdir}/msi_{params.case_id} {output.msi_result};
sed 's/\%/MSI/g' {params.tmpdir}/msi_{params.case_id} > {output.msi_result};

rm -rf {params.tmpdir};
"""
2 changes: 1 addition & 1 deletion BALSAMIC/snakemake_rules/report/generate_pdf.rule
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Expand Up @@ -56,7 +56,7 @@ rule msi_to_pdf:
"Converting MSI TXT file to PDF"
shell:
"""
python "{params.csv_to_pdf_script}" "{input.msi_result}" "{output.msi_result_pdf}" --delimiter "\t"
python "{params.csv_to_pdf_script}" "{input.msi_result}" "{output.msi_result_pdf}" --delimiter "\t" --header
"""

rule image_to_pdf:
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2 changes: 2 additions & 0 deletions CHANGELOG.rst
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Expand Up @@ -22,6 +22,8 @@ Removed:
Fixed:
^^^^^^
* Corrected tool name in deduplication metrics https://github.com/Clinical-Genomics/BALSAMIC/pull/1441
* MSI table https://github.com/Clinical-Genomics/BALSAMIC/pull/


[15.0.1]
--------
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2 changes: 1 addition & 1 deletion docs/balsamic_annotation.rst
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Expand Up @@ -222,7 +222,7 @@ See https://github.com/xjtu-omics/msisensor-pro/wiki for more details.
- all detected microsatellites
* - Number_of_Somatic_Sites
- the unstable(somatic) microsatellites
* - %
* - MSI
- The MSI score


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