diff --git a/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule b/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule index 4aba77fa4..ee632501b 100644 --- a/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule +++ b/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule @@ -226,8 +226,8 @@ rule svdb_merge_tumor_normal: tumor = get_sample_type(config["samples"], "tumor"), normal = get_sample_type(config["samples"], "normal"), case_name = config["analysis"]["case_id"], - vcf= lambda wildcards, input:[input[index] + ":" + svdb_sv_callers_to_merge_prio[index] for index in range(0,len(input))], - svdb_priority= ",".join(svdb_sv_callers_to_merge_prio) + vcf= lambda wildcards, input:[input[index] + ":" + svdb_callers_prio[index] for index in range(0,len(input))], + svdb_priority= ",".join(svdb_callers_prio) threads: get_threads(cluster_config, "svdb_merge_tumor_normal") message: diff --git a/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule b/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule index 0a0774f6c..3787002a4 100644 --- a/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule +++ b/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule @@ -122,8 +122,8 @@ rule svdb_merge_tumor_only: params: tumor = get_sample_type(config["samples"], "tumor"), case_name = config["analysis"]["case_id"], - vcf= lambda wildcards, input:[input[index] + ":" + svdb_sv_callers_to_merge_prio[index] for index in range(0,len(input))], - svdb_priority= ",".join(svdb_sv_callers_to_merge_prio) + vcf= lambda wildcards, input:[input[index] + ":" + svdb_callers_prio[index] for index in range(0,len(input))], + svdb_priority= ",".join(svdb_callers_prio) threads: get_threads(cluster_config, "svdb_merge_tumor_only") message: diff --git a/BALSAMIC/workflows/balsamic.smk b/BALSAMIC/workflows/balsamic.smk index e77e6d3a2..877cf7150 100644 --- a/BALSAMIC/workflows/balsamic.smk +++ b/BALSAMIC/workflows/balsamic.smk @@ -186,7 +186,7 @@ somatic_caller_cnv = get_variant_callers(config=config, sequencing_type=config["analysis"]["sequencing_type"], mutation_class="somatic") somatic_caller_sv.remove("svdb") -svdb_sv_callers_to_merge_prio = somatic_caller_sv + somatic_caller_cnv +svdb_callers_prio = somatic_caller_sv + somatic_caller_cnv # Collect only snv callers for calculating tmb somatic_caller_tmb = []