Merge pull request #493 from genomic-medicine-sweden/report_fusion_cl…

…eanup refactor: cleanup code
genomic-medicine-sweden · Sep 30, 2024 · 7dd36df · 7dd36df
2 parents 7241509 + ff962a4
commit 7dd36df
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -235,7 +235,7 @@ use rule gatk_mutect2_gvcf from snv_indels as snv_indels_gatk_mutect2_gvcf with:
 module annotation:
     snakefile:
         #get_module_snakefile(config, "hydra-genetics/annotation", path="workflow/Snakefile", tag="v0.1.0")
-        get_module_snakefile(config, "hydra-genetics/annotation", path="workflow/Snakefile", tag="50726ba")
+        get_module_snakefile(config, "hydra-genetics/annotation", path="workflow/Snakefile", tag="2956d59")
     config:
         config
 

diff --git a/workflow/scripts/report_fusions.py b/workflow/scripts/report_fusions.py
@@ -360,13 +360,13 @@
     flag_coverage1 = False
     flag_coverage2 = False
     if len(breakpoint1.split(":")) == 2:
-        chrom1 = fusion_dict[break_points][caller][7].split(":")[0]
-        pos1 = int(fusion_dict[break_points][caller][7].split(":")[1])
+        chrom1 = breakpoint1.split(":")[0]
+        pos1 = int(breakpoint1.split(":")[1])
     else:
         flag_coverage1 = True
     if len(breakpoint2.split(":")) == 2:
-        chrom2 = fusion_dict[break_points][caller][8].split(":")[0]
-        pos2 = int(fusion_dict[break_points][caller][8].split(":")[1])
+        chrom2 = breakpoint2.split(":")[0]
+        pos2 = int(breakpoint2.split(":")[1])
     else:
         flag_coverage2 = True
     for exon in dedup_coverage_list: