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fix: add .get() for optional values in config instead of dict access #118

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Merged
merged 2 commits into from
Apr 11, 2025
Merged

fix: add .get() for optional values in config instead of dict access #118

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4cf693d
fix: add .get() for optional values in config instead of dictionary a…
BiancaStoecker Apr 10, 2025
c6a6b7f
fix: remove superfluous == True
BiancaStoecker Apr 11, 2025
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24 changes: 12 additions & 12 deletions workflow/rules/common.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -208,9 +208,9 @@ def get_callset(wildcards):
vcf = callset["path"]
if get_somatic_status(wildcards):
return "results/normalized-variants/{callset}.gt-added.vcf.gz"
elif callset.get("rename-contigs", False) != False:
elif callset.get("rename-contigs", False):
return "results/normalized-variants/{callset}.replaced-contigs.vcf.gz"
elif callset["genome-build"] == "grch37":
elif callset.get("genome-build", "grch38") == "grch37":
return "results/normalized-variants/{callset}.lifted.vcf.gz"
elif isinstance(vcf, dict):
return "results/merge-callsets/{callset}.merged.vcf.gz"
Expand All @@ -221,9 +221,9 @@ def get_callset(wildcards):
def get_callset_correct_contigs(wildcards):
callset = config["variant-calls"][wildcards.callset]
vcf = callset["path"]
if "rename-contigs" in callset:
if callset.get("rename-contigs", False):
return "results/normalized-variants/{callset}.replaced-contigs.vcf.gz"
elif callset["genome-build"] == "grch37":
elif callset.get("genome-build", "grch38") == "grch37":
return "results/normalized-variants/{callset}.lifted.vcf.gz"
elif isinstance(vcf, dict):
return "results/merge-callsets/{callset}.merged.vcf.gz"
Expand All @@ -234,9 +234,9 @@ def get_callset_correct_contigs(wildcards):
def get_callset_correct_contigs_liftover(wildcards):
callset = config["variant-calls"][wildcards.callset]
vcf = callset["path"]
if callset["genome-build"] == "grch37":
if callset.get("genome-build", "grch38") == "grch37":
return "results/normalized-variants/{callset}.lifted.vcf.gz"
elif callset.get("rename-contigs", False) != False:
elif callset.get("rename-contigs", False):
return "results/normalized-variants/{callset}.replaced-contigs.vcf.gz"
elif isinstance(vcf, dict):
return "results/merge-callsets/{callset}.merged.vcf.gz"
Expand Down Expand Up @@ -388,17 +388,17 @@ def get_test_regions(wildcards):


def get_rename_contig_file(wildcards):
if config["variant-calls"][wildcards.callset][
"genome-build"
] == "grch37" and config["variant-calls"][wildcards.callset].get(
if config["variant-calls"][wildcards.callset].get(
"genome-build", "grch38"
) == "grch37" and config["variant-calls"][wildcards.callset].get(
"rename-contigs", False
):
return workflow.source_path(
"../resources/rename-contigs/grch37_ucsc2ensembl.txt"
)
if config["variant-calls"][wildcards.callset][
"genome-build"
] == "grch38" and config["variant-calls"][wildcards.callset].get(
if config["variant-calls"][wildcards.callset].get(
"genome-build", "grch38"
) == "grch38" and config["variant-calls"][wildcards.callset].get(
"rename-contigs", False
):
return workflow.source_path(
Expand Down