Merge pull request #70 from CCBR/fix/merge_callers

fix: final somatic merge
CCBR · Jan 10, 2024 · 54b2c02 · 54b2c02
2 parents 1336a86 + 492a2a8
commit 54b2c02
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Showing 2 changed files with 1 addition and 3 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -356,7 +356,7 @@ samples_for_caller_merge=[]
 merge_callers_args=dict.fromkeys(pairs_ids)
 merge_callers_rodlist=",".join(caller_list)
 if (len(caller_list) >= 1):
-    merge_callers_args_list = [["--variant:{} {}/{}/{}.FINAL.vcf".format(re.sub("_out","",vc_out), os.path.join(output_somatic_snpindels, vc_out),"vcf",pair_id) for vc_out in somatic_callers_dirs] for pair_id in pairs_ids]
+    merge_callers_args_list = [["--variant:{} {}/{}/{}.FINAL.norm.vcf".format(re.sub("_out","",vc_out), os.path.join(output_somatic_snpindels, vc_out),"vcf",pair_id) for vc_out in somatic_callers_dirs] for pair_id in pairs_ids]
     merge_callers_args = dict(zip(pairs_ids, [" ".join(arglist) for arglist in merge_callers_args_list]))
     samples_for_caller_merge=pairs_ids
     somatic_callers_dirs=list(somatic_callers_dirs + [merge_outdir])

diff --git a/workflow/rules/somatic_snps.common.smk b/workflow/rules/somatic_snps.common.smk
@@ -168,8 +168,6 @@ rule somatic_merge_callers:
       mkdir -p "$(dirname {output.mergedvcf})"
     fi
 
-    input_str="--variant $(echo "{input.vcf}" | sed -e 's/ / --variant /g')"
-
     java -Xmx60g -Djava.io.tmpdir=${{tmp}} -jar $GATK_JAR -T CombineVariants \\
         -R {params.genome} \\
         -nt {threads} \\