From b6631aa52d212d70e435355650b8c25022ed791f Mon Sep 17 00:00:00 2001 From: Khurram Maqbool Date: Thu, 29 Jul 2021 22:48:31 +0200 Subject: [PATCH] Fix delly --- .../snakemake_rules/variant_calling/somatic_sv_tumor_only.rule | 3 ++- BALSAMIC/utils/models.py | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) 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 1034adef8..ac2f42fcb 100644 --- a/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule +++ b/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule @@ -55,7 +55,8 @@ rule delly_tumor_only: bamT = bam_dir + tumor_bam, excl = config["reference"]["delly_exclusion_converted"], output: - final = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".delly.vcf.gz" + final = vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".delly.vcf.gz", + namemap= vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".delly.sample_name_map", benchmark: benchmark_dir + 'delly_tumor_only_' + config["analysis"]["case_id"] + "_delly.tsv" singularity: diff --git a/BALSAMIC/utils/models.py b/BALSAMIC/utils/models.py index 8c954267d..4144bb4e5 100644 --- a/BALSAMIC/utils/models.py +++ b/BALSAMIC/utils/models.py @@ -162,7 +162,7 @@ class VCFModel(BaseModel): manta_germline: VarcallerAttribute haplotypecaller: VarcallerAttribute TNscope_umi: VarcallerAttribute - delly: VarcallerAttribute +# delly: VarcallerAttribute class AnalysisModel(BaseModel): """Pydantic model containing workflow variables