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Fix/delly not showing in workflow at runtime #698

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Aug 2, 2021
Merged

Fix/delly not showing in workflow at runtime #698

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fb3334a
Fix delly run
khurrammaqbool Jul 29, 2021
060cec3
changelog
khurrammaqbool Jul 29, 2021
b6631aa
Fix delly
khurrammaqbool Jul 29, 2021
81668fa
fix delly models and vep
khurrammaqbool Jul 30, 2021
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2 changes: 1 addition & 1 deletion BALSAMIC/utils/models.py
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Expand Up @@ -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
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5 changes: 3 additions & 2 deletions BALSAMIC/workflows/balsamic.smk
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Expand Up @@ -363,12 +363,13 @@ else:
analysis_specific_results.extend([expand(vep_dir + "{vcf}.all.filtered.pass.vcf.gz",
vcf=get_vcf(config, ["manta"], [config["analysis"]["case_id"]]))])

analysis_specific_results.extend([expand(vcf_dir + "{vcf}.vcf.gz",
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vcf=get_vcf(config, ["delly"],[config["analysis"]["case_id"]]))])

if config["analysis"]["sequencing_type"] == "wgs" and config['analysis']['analysis_type'] == "single":
if "dragen" in config:
analysis_specific_results.extend([Path(result_dir, "dragen", "SNV.somatic." + config["analysis"]["case_id"] + ".dragen_tumor.bam").as_posix(),
Path(result_dir, "dragen", "SNV.somatic." + config["analysis"]["case_id"] + ".dragen.vcf.gz").as_posix()])
# delly get vcf file
analysis_specific_results.extend([Path(vcf_dir + "SV.somatic." + config["analysis"]["case_id"] + ".delly.vcf.gz")])

for r in config["rules"]:
include: Path(RULE_DIRECTORY, r).as_posix()
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