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change var name
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khurrammaqbool committed Mar 14, 2022
1 parent 18b3de9 commit 880e860
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Showing 3 changed files with 5 additions and 5 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -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:
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion BALSAMIC/workflows/balsamic.smk
Original file line number Diff line number Diff line change
Expand Up @@ -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 = []
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