fix: update MSI table (#1459)

* update MSI table * changelog
Clinical-Genomics · Jun 28, 2024 · 8ab0e4d · 8ab0e4d
1 parent 6f48313
commit 8ab0e4d
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diff --git a/BALSAMIC/snakemake_rules/annotation/msi_tumor_normal.rule b/BALSAMIC/snakemake_rules/annotation/msi_tumor_normal.rule
@@ -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};
     """
diff --git a/BALSAMIC/snakemake_rules/report/generate_pdf.rule b/BALSAMIC/snakemake_rules/report/generate_pdf.rule
@@ -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:

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -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/1459
+
 
 [15.0.1]
 --------

diff --git a/docs/balsamic_annotation.rst b/docs/balsamic_annotation.rst
@@ -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
-Original file line number
+Diff line change
@@ 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/1459
     [15.0.1]
     --------
@@ Expand Down @@