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fix: eb_filter wrapper assuming ANN/CSQ is present #506

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merged 10 commits into from
May 6, 2024
Merged

fix: eb_filter wrapper assuming ANN/CSQ is present #506

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8361af9
fix: missing check for has_annotation in somatic_variant_filtration r…
tedil Apr 29, 2024
ad5f93e
fix: ebfilter expression depends on ann field presence
tedil Apr 29, 2024
d3181b4
fmt
tedil Apr 29, 2024
0d0b513
fix: ebfilter expression depends on ann field presence
tedil Apr 29, 2024
5846aa3
Merge branch 'fix-eb-filter-nonexistent-ann' of github.com:bihealth/s…
tedil Apr 29, 2024
02508a7
quote has_annotation
tedil Apr 29, 2024
d30fa30
quote has_annotation
tedil Apr 29, 2024
b6315af
Merge branch 'fix-eb-filter-nonexistent-ann' of github.com:bihealth/s…
tedil Apr 29, 2024
3b22e0d
merge main into fix-eb-filter-nonexistent-ann, move has_annotation ch…
tedil May 6, 2024
43c74a0
include 'has_annotation' param in ebfilter test
tedil May 6, 2024
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2 changes: 2 additions & 0 deletions snappy_pipeline/workflows/somatic_variant_filtration/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -410,6 +410,7 @@ def input_function(wildcards):
filter_nb = int(wildcards["filter_nb"])
ebfilter_config = self.config["filter_list"][filter_nb - 1][self.filter_name]
parameters.update(ebfilter_config)
parameters["has_annotation"] = self.config.get("has_annotation", False)
return parameters

return input_function
Expand Down Expand Up @@ -731,6 +732,7 @@ def get_params(self, action):
self._validate_action(action)
parameters = self.config["eb_filter"]
parameters.update(self.config["filter_sets"]["dkfz_and_ebfilter"])
parameters["has_annotation"] = self.config.get("has_annotation", False)
return parameters

@dictify
Expand Down
7 changes: 6 additions & 1 deletion snappy_wrappers/wrappers/eb_filter/wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@

params = dict(snakemake.params)["args"]
filter_name = params["filter_name"] if "filter_name" in params else ""
has_annotation = str(params["has_annotation"] if "has_annotation" in params else False)

if "interval" in params:
cmd_fetch = "tabix --print-header {} {}".format(
Expand Down Expand Up @@ -61,7 +62,11 @@
filter=$(echo "$filter" | sed -e "s/^ || //")
ann="CSQ"
zgrep -q "^##INFO=<ID=CSQ," {snakemake.input.vcf} || ann="ANN"
filter="$filter || $ann ~ \"stream_gene_variant\""
if [[ '{has_annotation}' == "True" ]]; then
filter="$filter || $ann ~ \"stream_gene_variant\""
else
filter="$filter"
fi
{cmd_fetch} \
| bcftools view \
-e "$filter" \
Expand Down
2 changes: 1 addition & 1 deletion tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py
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Expand Up @@ -562,7 +562,7 @@ def test_one_filter_step_part_get_params(somatic_variant_filtration_workflow_lis
assert actual == expected

wildcards = Wildcards(fromdict={"filter_nb": 2})
expected = {"filter_name": "ebfilter_2", "threshold": 2.3}
expected = {"filter_name": "ebfilter_2", "threshold": 2.3, "has_annotation": True}
actual = somatic_variant_filtration_workflow_list.get_params("one_ebfilter", "run")(wildcards)
assert actual == expected

Expand Down
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