diff --git a/workflow/Snakefile b/workflow/Snakefile index 5885be9..0e57b04 100644 --- 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 index 47f79e6..20400c6 100644 --- 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} \\