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fix: handle reference creation with unit file containing both T and N #361

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Nov 3, 2023
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3 changes: 3 additions & 0 deletions config/config_references.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,9 @@ purecn_coverage_list:
container: "docker://hydragenetics/purecn:2.2.0"
genome: hg19

purecn_interval_file:
container: "docker://hydragenetics/purecn:2.2.0"

purecn_normal_db:
container: "docker://hydragenetics/purecn:2.2.0"

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5 changes: 5 additions & 0 deletions workflow/Snakefile_references.smk
Original file line number Diff line number Diff line change
Expand Up @@ -142,6 +142,11 @@ use rule cnvkit_build_normal_reference from references as references_cnvkit_buil
antitarget="references/cnvkit_create_anti_targets/cnvkit_manifest.antitarget.bed",
ref=config.get("reference", {}).get("fasta", ""),
mappability=config.get("reference", {}).get("mappability", ""),
output:
PoN=temp("references/cnvkit_build_normal_reference/cnvkit.PoN.cnn"),
tmp_bed=temp("cnvkit_manifest.target.target.bed"),
tmp_target_cov=temp(get_cnvkit_target(units, "cnvkit_pon")),
tmp_antitarget_cov=temp(get_cnvkit_antitarget(units, "cnvkit_pon")),


####################################################
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8 changes: 8 additions & 0 deletions workflow/rules/common_references.smk
Original file line number Diff line number Diff line change
Expand Up @@ -132,6 +132,14 @@ def get_cnv_vcfs(units: pandas.DataFrame, name: str) -> typing.List[str]:
return get_files(units, name, "cnv_sv/svdb_query/%s_%s.pathology_purecn.svdb_query.vcf")


def get_cnvkit_target(units: pandas.DataFrame, name: str) -> typing.List[str]:
return get_files(units, name, "%s_%s.targetcoverage.cnn")


def get_cnvkit_antitarget(units: pandas.DataFrame, name: str) -> typing.List[str]:
return get_files(units, name, "%s_%s.antitargetcoverage.cnn")


def get_files(units: pandas.DataFrame, name: str, string_path: str):
types = []
for i in output_spec["files"]:
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