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fix: integration of gcnv and melt into sv_calling_wgs #350

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merged 4 commits into from
Jan 16, 2023
Merged

fix: integration of gcnv and melt into sv_calling_wgs #350

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aaa09aa
fix: integration of gcnv and melt into sv_calling_wgs
holtgrewe Jan 16, 2023
a14f446
fix
holtgrewe Jan 16, 2023
c005f11
snakefmt
holtgrewe Jan 16, 2023
ba96aa5
wip
holtgrewe Jan 16, 2023
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2 changes: 1 addition & 1 deletion snappy_pipeline/workflows/common/gcnv/gcnv_run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -516,7 +516,7 @@ def get_result_files(self):

The function will skip pedigrees where samples have inconsistent library kits and print a warning.
"""
if "gcnv" not in self.config["tools"]:
if "gcnv" not in self.config["tools"] and "gcnv" not in self.config["tools"].get("dna", {}):
return

# Get list with all result path template strings.
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4 changes: 3 additions & 1 deletion snappy_pipeline/workflows/common/sv_calling.py
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Expand Up @@ -17,7 +17,9 @@ def get_result_files(self):
The implementation will return a list of all paths with prefix ``output/` that are
returned by ``self.get_output_files()`` for all actions in ``self.actions``.
"""
if self.name not in self.config["tools"]:
if self.name not in self.config["tools"] and not (
hasattr(self.config, "tools") and self.name in self.config["tools"].get("dna", {})
):
return # tool not enabled, no result files

ngs_mapping_config = DictQuery(self.w_config).get("step_config/ngs_mapping")
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